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IFB French Institute of Bioinformatics

The French Institute of Bioinformatics (CNRS IFB) is a national service infrastructure in bioinformatics. IFB’s principal mission is to provide basic services and resources in bioinformatics for scientists and engineers working in the life sciences. IFB is the French node of the European research infrastructure, ELIXIR.

IFB French Institute of Bioinformatics https://tess.elixir-europe.org/content_providers/ifb-french-institute-of-bioinformatics The French Institute of Bioinformatics (CNRS IFB) is a national service infrastructure in bioinformatics. IFB’s principal mission is to provide basic services and resources in bioinformatics for scientists and engineers working in the life sciences. IFB is the French node of the European research infrastructure, ELIXIR. /system/content_providers/images/000/000/049/original/ifb-logo_1.png?1469458221
Showing 97 materials out of 97. View all results.
Variant Filtering

Some use cases : - Extract a subset of variants (localization, type) - Combine variants from several analyses - Compare obtained variants from several data types (RNA ...

Keywords: Genomics

Variant Filtering https://tess.elixir-europe.org/materials/variant-filtering Some use cases : - Extract a subset of variants (localization, type) - Combine variants from several analyses - Compare obtained variants from several data types (RNA ... Genomics
Galaxy III: Visualization

Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV)

Keywords: Genomics

Galaxy III: Visualization https://tess.elixir-europe.org/materials/galaxy-iii-visualization Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV) Genomics
Docker for Beginners

What is Docker? Building an image BioShadock Orchestration

Keywords: Docker

Docker for Beginners https://tess.elixir-europe.org/materials/docker-for-beginners What is Docker? Building an image BioShadock Orchestration Docker
Revealing and analyzing microbial networks: from topology to functional behaviors

Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated...

Keywords: metagenomics

Revealing and analyzing microbial networks: from topology to functional behaviors https://tess.elixir-europe.org/materials/revealing-and-analyzing-microbial-networks-from-topology-to-functional-behaviors-14d83c7f-c5f9-4738-8cd5-42e48a1088f7 Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete. Within this seminar, we will illustrate two complementary approaches that aim to overcome these points in different manners. metagenomics 2016-12-16 2017-01-11
NGS data exploration with the MicroScope Platform

Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools

Keywords: Genomics, NGS, RNA-seq, SNP, Transcriptomics

NGS data exploration with the MicroScope Platform https://tess.elixir-europe.org/materials/ngs-data-exploration-with-the-microscope-platform Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools Genomics, NGS, RNA-seq, SNP, Transcriptomics
BioBlend API

BioBlend module, a python library to use Galaxy API

Keywords: API, Galaxy, Python

BioBlend API https://tess.elixir-europe.org/materials/bioblend-api BioBlend module, a python library to use Galaxy API API, Galaxy, Python
Variants: alignment and pre-treatment; GATK

Variant calling practical session

Keywords: Genomics

Variants: alignment and pre-treatment; GATK https://tess.elixir-europe.org/materials/variants-alignment-and-pre-treatment-gatk Variant calling practical session Genomics
Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a...

Keywords: metagenomics

Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses https://tess.elixir-europe.org/materials/who-is-doing-what-on-the-cheese-surface-overview-of-the-cheese-microbial-ecosystem-functioning-by-metatranscriptomic-analyses-55c4b5d0-ba6e-4ae0-879f-7bc27c10b3eb Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We used an iterative sensory procedure to select a simplified microbial consortium, composed of only nine species (three yeasts and six bacteria), producing the odor of Livarot-type cheese when inoculated in a sterile cheese curd. All the genomes were sequenced in order to determine the functional capacities of the different species and facilitate RNA-Seq data analyses. We followed the ripening process of experimental cheeses made using this consortium during four weeks, by metatranscriptomic and biochemical analyses. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. We next applied the same approach to investigate the activity of the microorganisms in real cheeses, namely Reblochon-style cheeses. This provided useful insights into the physiological changes that occur during cheese ripening, such as changes in energy substrates, anabolic reactions, or stresses. metagenomics 2016-12-15 2017-01-11
Visualization of NGS data with IGV

Visualisation of next-gen sequencing data with Integrative Genomics Viewer

Keywords: Data visualization, Genomics, NGS

Visualization of NGS data with IGV https://tess.elixir-europe.org/materials/visualization-of-ngs-data-with-igv Visualisation of next-gen sequencing data with Integrative Genomics Viewer Data visualization, Genomics, NGS
Dr Jekyll and Mr Hyde: The dual face of metagenomics in phylogenetic analysis

The aim of this lecture is to present the impact of metagenomics and single-cell genomics on public databases. These new powerful approches allow us to have access to the diversity of life on our planet. However, care has to be taken when using these data for posterior analyses, such as...

Keywords: metagenomics

Dr Jekyll and Mr Hyde: The dual face of metagenomics in phylogenetic analysis https://tess.elixir-europe.org/materials/dr-jekyll-and-mr-hyde-the-dual-face-of-metagenomics-in-phylogenetic-analysis-2a7d1d11-5a75-4365-b6bd-c48c8ad9a5dd The aim of this lecture is to present the impact of metagenomics and single-cell genomics on public databases. These new powerful approches allow us to have access to the diversity of life on our planet. However, care has to be taken when using these data for posterior analyses, such as phylogenetic studies, as critical errors can still be present in the databases. This course will incorporate examples taken from real studies, and we will investigate methods used for error detection. metagenomics 2016-12-16 2017-01-11
A Simple Phylogenetic Tree Construction (part 2)

Understand the method used in identifying an unknown sequence. Understand the limitations of this method Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)

Keywords: Phylogenetics

A Simple Phylogenetic Tree Construction (part 2) https://tess.elixir-europe.org/materials/a-simple-phylogenetic-tree-construction-part-2 Understand the method used in identifying an unknown sequence. Understand the limitations of this method Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot) Phylogenetics
Tool development and integration into Galaxy

Questions: What is a tool for Galaxy? How to build a tool/wrapper with the good practices? How to deal with the tool environment? Objectives: Discover what is a wrapper and its structure Use the Planemo utilities to develop a good wrapper Deal with the dependencies Write functional...

Keywords: Galaxy

Tool development and integration into Galaxy https://tess.elixir-europe.org/materials/tool-development-and-integration-into-galaxy Questions: What is a tool for Galaxy? How to build a tool/wrapper with the good practices? How to deal with the tool environment? Objectives: Discover what is a wrapper and its structure Use the Planemo utilities to develop a good wrapper Deal with the dependencies Write functional tests Make a tool ready for publishing in a ToolShed Galaxy
HOVERGEN tutorial

HOVERGEN is a database containing homologous vertebrate protein and nucleotide sequences. It allows to easily select similar gene sequences from a wide range of vertebrates. Hence it becomes particularly useful in comparative genomics, phylogeny and evolutionary studies on a molecular level....

Keywords: genomics, proteomics

HOVERGEN tutorial https://tess.elixir-europe.org/materials/hovergen-tutorial HOVERGEN is a database containing homologous vertebrate protein and nucleotide sequences. It allows to easily select similar gene sequences from a wide range of vertebrates. Hence it becomes particularly useful in comparative genomics, phylogeny and evolutionary studies on a molecular level. HOVERGEN Clean contains only complete sequences which reattach to their family. Hence its library is smaller, but more reliable. genomics, proteomics
Exploring Microscope Platform

How to use the Microscope Platform to annotate and analyze microbial genomes.

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics

Exploring Microscope Platform https://tess.elixir-europe.org/materials/exploring-microscope-platform How to use the Microscope Platform to annotate and analyze microbial genomes. Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics
RGP finder: prediction of Genomic Islands

Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization

Keywords: CDS, Data visualization, Genomics, RGP

RGP finder: prediction of Genomic Islands https://tess.elixir-europe.org/materials/rgp-finder-prediction-of-genomic-islands Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization CDS, Data visualization, Genomics, RGP
Soil metagenomics, potential and pitfalls

The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation)....

Keywords: metagenomics

Soil metagenomics, potential and pitfalls https://tess.elixir-europe.org/materials/soil-metagenomics-potential-and-pitfalls-04d3bb46-36ba-47c0-9993-9c7d0aacad32 The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation). Nevertheless, genome structure information has been restricted by a large extent to a small fraction of cultivated species. This limitation can be circumvented now by modern alternative approaches including metagenomics or single cell genomics. Metagenomics includes the data treatment of DNA sequences from many members of the microbial community, in order to either extract a specific microorganism’s genome sequence or to evaluate the community function based on the relative quantities of different gene families. In my talk I will show how these metagenomic datasets can be used to estimate and compare the functional potential of microbial communities from various environments with a special focus on antibiotic resistance genes. However, metagenomic datasets can also in some cases be partially assembled into longer sequences representing microbial genetic structures for trying to correlate different functions to their co-location on the same genetic structure. I will show how the microbial community composition of a natural grassland soil characterized by extremely high microbial diversity could be managed for sequentially attempt to reconstruct some bacterial genomes. Metagenomics can also be used to exploit the genetic potential of environmental microorganisms. I will present an integrative approach coupling rrs phylochip and high throughput shotgun sequencing to investigate the shift in bacterial community structure and functions after incubation with chitin. In a second step, these functions of potential industrial interest can be discovered by using hybridization of soil metagenomic DNA clones spotted on high density membranes by a mix of oligonucleotide probes designed to target genes encoding for these enzymes. After affiliation of the positive hybridizing spots to the corresponding clones in the metagenomic library the inserts are sequenced, DNA assembled and annotated leading to identify new coding DNA sequences related to genes of interest with a good coverage but a low similarity against closest hits in the databases confirming novelty of the detected and cloned genes. metagenomics 2016-12-16 2017-01-11
Transcriptome de novo assembly

Not available

Keywords: Transcriptomics

Transcriptome de novo assembly https://tess.elixir-europe.org/materials/transcriptome-de-novo-assembly Not available Transcriptomics
Galaxy Installation

How to install a local instance of Galaxy

Keywords: Galaxy

Galaxy Installation https://tess.elixir-europe.org/materials/galaxy-installation How to install a local instance of Galaxy Galaxy
RNA-Seq: isoform detection and quantification

transcriptome from new condition tissue-speci c transcriptome different development stages transcriptome from non model organism cancer cell RNA maturation mutant How to manage RNA-Seq data with genes subjected to di erential splicing? Is it possible to discover new isoforms? Is it...

Keywords: Isoforms, RNA-seq, Transcriptomics

RNA-Seq: isoform detection and quantification https://tess.elixir-europe.org/materials/rna-seq-isoform-detection-and-quantification transcriptome from new condition tissue-speci c transcriptome different development stages transcriptome from non model organism cancer cell RNA maturation mutant How to manage RNA-Seq data with genes subjected to di erential splicing? Is it possible to discover new isoforms? Is it possible to quantify abundance of each isoform Isoforms, RNA-seq, Transcriptomics
Variant Filtering

Use cases: Extact a subset of variants Combine variants from several analysis Compare obtained variants from several data types Identify new variants compare to a reference list Apply specific filters for Chip Design

Keywords: NGS, Variant calling

Variant Filtering https://tess.elixir-europe.org/materials/variant-filtering-98171288-9eb3-49d3-b627-8ae1ead26885 Use cases: Extact a subset of variants Combine variants from several analysis Compare obtained variants from several data types Identify new variants compare to a reference list Apply specific filters for Chip Design NGS, Variant calling
Gut metagenomics in cardiometabolic diseases

Cardio-metabolic and Nutrition-related diseases (CMDs) represent an enormous burden for health care. They are characterized by very heterogeneous phenotypes progressing with time. It is virtually impossible to predict who will or will not develop cardiovascular comorbidities. There is a clear...

Keywords: metagenomics

Gut metagenomics in cardiometabolic diseases https://tess.elixir-europe.org/materials/gut-metagenomics-in-cardiometabolic-diseases-339bc8b2-0c05-4f21-9aba-2ae647a5178c Cardio-metabolic and Nutrition-related diseases (CMDs) represent an enormous burden for health care. They are characterized by very heterogeneous phenotypes progressing with time. It is virtually impossible to predict who will or will not develop cardiovascular comorbidities. There is a clear need to intervene earlier in the natural cycle of the disease, before irreversible tissue damages develop. Predictive tools still remain elusive and environmental factors (food, nutrition, physical activity and psychosocial factors) play major roles in the development of these interrelated pathologies. Poor nutritional environment and lifestyle also promote health deterioration resulting in CMD progression. In the last few years, the characterization of the gut microbiome (i.e. collective bacteria genome) and gut-derived molecules (i.e. metabolites, lipids, inflammatory molecules) has opened up new avenues for the generation of fundamental knowledge regarding putative shared pathways in CMD. The gut microbiome is likely to have an even greater impact than genetic factors given its close relationship with environmental factors. In metabolic disorders, the discoveries that low bacterial gene richness associates with cardiovascular risks stimulate encourage these developments. Due to the complexity of the gut microbiome, and its interactions with human (host) metabolism as well as with the immune system, it is only through integrative analyses where metabolic network models are used as scaffold for analysis that it will be possible to identify markers and shared pathways, which will contribute to improve patient stratification and develop new modes of patient care. metagenomics 2016-12-15 2017-01-11
Exercices on Galaxy: metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Exercices on Galaxy: metagenomics https://tess.elixir-europe.org/materials/exercices-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
Galaxy Handlers

Galaxy is a web application that uses handlers to perform actions. There are two main types of actions that are carried out by handlers: Respond to user requests; These actions are carried out by web handlers Manage the execution of tools; These actions are performed by job handlers. By...

Keywords: Galaxy

Galaxy Handlers https://tess.elixir-europe.org/materials/galaxy-handlers Galaxy is a web application that uses handlers to perform actions. There are two main types of actions that are carried out by handlers: Respond to user requests; These actions are carried out by web handlers Manage the execution of tools; These actions are performed by job handlers. By default, Galaxy is configured to run a single handler that handles both user queries and jobs. Depending on the number of users accessing your Galaxy instance or the number of jobs you need to manage you may need to start web handlers or additional job handlers. Galaxy
New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology

It is a generally accepted characteristic of the biogeochemical nitrogen cycle that nitrification is catalyzed by two distinct clades of microorganisms. First, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite, which subsequently is oxidized to nitrate by nitrite-oxidizing...

Keywords: metagenomics

New perspectives on nitrite-oxidizing bacteria - linking genomes to physiology https://tess.elixir-europe.org/materials/new-perspectives-on-nitrite-oxidizing-bacteria-linking-genomes-to-physiology-6bc8b25e-043d-47f1-b184-c776d595fb7b It is a generally accepted characteristic of the biogeochemical nitrogen cycle that nitrification is catalyzed by two distinct clades of microorganisms. First, ammonia-oxidizing bacteria and archaea convert ammonia to nitrite, which subsequently is oxidized to nitrate by nitrite-oxidizing bacteria (NOB). The latter were traditionally perceived as physiologically restricted organisms and were less intensively studied than other nitrogen-cycling microorganisms. This picture is contrasted by new discoveries of an unexpected high diversity of mostly uncultured NOB and a great physiological versatility, which includes complex microbe-microbe interactions and lifestyles outside the nitrogen cycle. Most surprisingly, close relatives to NOB perform complete nitrification (ammonia oxidation to nitrate), a process that had been postulated to occur under conditions selecting for low growth rates but high growth yields. The existence of Nitrospira species that encode all genes required for ammonia and nitrite oxidation was first detected by metagenomic analyses of an enrichment culture for nitrogen-transforming microorganisms sampled from the anoxic compartment of a recirculating aquaculture system biofilter. Batch incubations and FISH-MAR experiments showed that these Nitrospira indeed formed nitrate from the aerobic oxidation of ammonia, and used the energy derived from complete nitrification for carbon fixation, thus proving that they indeed represented the long-sought-after comammox organisms. Their ammonia monooxygenase (AMO) enzymes were distinct from canonical AMOs, therefore rendering recent horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. Instead, their AMO displayed highest similarities to the “unusual” particulate methane monooxygenase from Crenothrix polyspora, thus shedding new light onto the function of this sequence group. This recognition of a novel AMO type indicates that a whole group of ammonia-oxidizing microorganisms has been overlooked, and will improve our understanding of the environmental abundance and distribution of this functional group. Data mining of publicly available metagenomes already indicated a widespread occurrence in natural and engineered environments like aquifers and paddy soils, and drinking and wastewater treatment systems. metagenomics 2016-12-16 2017-01-11
Galaxy Visualisation - Slides

Questions How can visualization plugins benefit science? Objectives Implement a first Galaxy visualization Understand the client side vs. server side principle

Keywords: Galaxy

Galaxy Visualisation - Slides https://tess.elixir-europe.org/materials/galaxy-visualisation-slides Questions How can visualization plugins benefit science? Objectives Implement a first Galaxy visualization Understand the client side vs. server side principle Galaxy
Galaxy Docker Training Tutorial

Galaxy docker integration Enable Galaxy to use BioContainers (Docker) Galaxy with Docker swarm

Keywords: Docker, Galaxy

Galaxy Docker Training Tutorial https://tess.elixir-europe.org/materials/galaxy-docker-training-tutorial Galaxy docker integration Enable Galaxy to use BioContainers (Docker) Galaxy with Docker swarm Docker, Galaxy
Deciphering the human intestinal tract microbiome using metagenomic computational methods

In 2010, the MetaHIT consortium published a 3.3M microbiota gene catalog generated by whole genome shotgun metagenomic sequencing, representing a mixture of bacteria, archaea, parasites and viruses coming from 124 human stool metagenomic samples [Qin et al, Nature 2010]. However most of the genes...

Keywords: metagenomics

Deciphering the human intestinal tract microbiome using metagenomic computational methods https://tess.elixir-europe.org/materials/deciphering-the-human-intestinal-tract-microbiome-using-metagenomic-computational-methods-5698849a-2061-466c-8dc6-abe487aa2733 In 2010, the MetaHIT consortium published a 3.3M microbiota gene catalog generated by whole genome shotgun metagenomic sequencing, representing a mixture of bacteria, archaea, parasites and viruses coming from 124 human stool metagenomic samples [Qin et al, Nature 2010]. However most of the genes were fragmented, taxonomically and functionally unknown, making it difficult to define and select biomarkers of interest for genome-wide association studies. Since that, this human gene catalog was improved multiple times, with the last update by [Li et al, Nature Biotechnology, 2014], which generated a 10M gene catalog using more than 1000 metagenomic samples and including some prevalent human microbe genome available at that time. Along with the catalog update, the scientific community developed new tools to challenge the complexity of this dataset and provided new ways to assemble, annotate, quantify and classify the genes coming from these catalogs. In this talk we will discuss the main approaches related to the computational treatment of the different gene catalog other the time, illustrated by the different papers that deciphered step by step the hidden information of our microbiota and his link with our health. metagenomics 2016-12-15 2017-01-11
Galaxy Interactive Tour

Questions What is a Galaxy Interactive Tour? How to create a Galaxy Interactive Tour? Objectives Discover what is a Galaxy Interactive Tour Be able to create a Galaxy Interactive Tour Be able to add a Galaxy Interactive Tour in a Galaxy instance

Keywords: Galaxy

Galaxy Interactive Tour https://tess.elixir-europe.org/materials/galaxy-interactive-tour Questions What is a Galaxy Interactive Tour? How to create a Galaxy Interactive Tour? Objectives Discover what is a Galaxy Interactive Tour Be able to create a Galaxy Interactive Tour Be able to add a Galaxy Interactive Tour in a Galaxy instance Galaxy
Isoform discovery and quanti cation from RNA-Seq data

Not available

Keywords: RNA-seq

Isoform discovery and quanti cation from RNA-Seq data https://tess.elixir-europe.org/materials/isoform-discovery-and-quanti-cation-from-rna-seq-data Not available RNA-seq
REPET: TEdannot Tutorial

TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo

Keywords: Annotation, Genomics

REPET: TEdannot Tutorial https://tess.elixir-europe.org/materials/repet-tedannot-tutorial TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo Annotation, Genomics
RNA-seq: Differential gene expression analysis

Transcriptome analysis provides information about the identity and quantity of all RNA molecules

Keywords: Genomics, RNA-seq

RNA-seq: Differential gene expression analysis https://tess.elixir-europe.org/materials/rna-seq-differential-gene-expression-analysis Transcriptome analysis provides information about the identity and quantity of all RNA molecules Genomics, RNA-seq
RADSeq Data Analysis

Introduction to RADSeq through STACKS on Galaxy

Keywords: NGS

RADSeq Data Analysis https://tess.elixir-europe.org/materials/radseq-data-analysis Introduction to RADSeq through STACKS on Galaxy NGS
Genomic copy number Analysis

No description available

Keywords: Copy number, Structural genomics

Genomic copy number Analysis https://tess.elixir-europe.org/materials/genomic-copy-number-analysis No description available Copy number, Structural genomics
Hidden in the permafrost

The last decade witnessed the discovery of four families of giant viruses infecting Acanthamoeba. They have genome encoding from 500 to 2000 genes, a large fraction of which encoding proteins of unknown origin. These unique proteins meant to recognize and manipulate the same building blocks as...

Keywords: metagenomics

Hidden in the permafrost https://tess.elixir-europe.org/materials/hidden-in-the-permafrost-c83267ed-68a6-4f10-b584-9f9eaae52009 The last decade witnessed the discovery of four families of giant viruses infecting Acanthamoeba. They have genome encoding from 500 to 2000 genes, a large fraction of which encoding proteins of unknown origin. These unique proteins meant to recognize and manipulate the same building blocks as cells raise the question on their origin as well as the role viruses played in the cellular word evolution. The Mimiviridae and the Pandoraviridae are increasingly populated by members from very diverse habitats and are ubiquitous on the planet. After prospecting the space, we went back in the past and isolated two other giant virus families from a 30,000 years old permafrost sample, Pithovirus and Mollivirus sibericum. A metagenomics study of the sample was performed to inventory its biodiversity and assess to what extend the host and the viruses were dominant. I will describe the two sequencing approaches which have been used and compare the results. 1: Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of Mimivirus. Science. 2004 Nov 19;306(5700):1344-50. 2: Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C. Pandoraviruses:amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science. 2013 Jul 19;341(6143):281-6. 3: Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4274-9. 4: Legendre M, Lartigue A, Bertaux L, Jeudy S, Bartoli J, Lescot M, Alempic JM, Ramus C, Bruley C, Labadie K, Shmakova L, Rivkina E, Couté Y, Abergel C, Claverie JM. In-depth study of Mollivirus sibericum, a new 30,000-y-old giant virus infecting Acanthamoeba. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):E5327-35. metagenomics 2016-12-16 2017-01-11
Galaxy Configuration Hierarchy

How to configure your local instance of Galaxy

Keywords: Galaxy

Galaxy Configuration Hierarchy https://tess.elixir-europe.org/materials/galaxy-configuration-hierarchy How to configure your local instance of Galaxy Galaxy
IFB Cloud tutorial: Gene regulation

1. Using the Gene-regulation appliance 1.1 Requirements 1.2 Virtual disk creation 1.3 Creation of an instance 1.4 Connection to the device 1.5 Download source data 1.6 Execute workflow 2. Visualizing results 2.1 Install and run the X2Go client on your host computer 2.2...

Keywords: Cloud Computing, Gene Regulation

IFB Cloud tutorial: Gene regulation https://tess.elixir-europe.org/materials/ifb-cloud-tutorial-gene-regulation-e10be4af-e097-44a0-a35c-f5ed0ef9fd45 1. Using the Gene-regulation appliance 1.1 Requirements 1.2 Virtual disk creation 1.3 Creation of an instance 1.4 Connection to the device 1.5 Download source data 1.6 Execute workflow 2. Visualizing results 2.1 Install and run the X2Go client on your host computer 2.2 Visualize results FastQC IGV 3. Create your own Gene-regulation appliance Creation of an instance Installing programs and dependencies Get the gene-regulation repository Run makefile to install the dependencies Cloud Computing, Gene Regulation
Chip-seq: Pattern Analysis tutorial

Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, NGS, Pattern recognition

Chip-seq: Pattern Analysis tutorial https://tess.elixir-europe.org/materials/chip-seq-pattern-analysis-tutorial Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, NGS, Pattern recognition
Chip-seq: Motif Analysis Tutorial

Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, Motif analysis, NGS, Pattern recognition

Chip-seq: Motif Analysis Tutorial https://tess.elixir-europe.org/materials/chip-seq-motif-analysis-tutorial Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, Motif analysis, NGS, Pattern recognition
Chip Seq: Annotation and visualization Lesson

How to add biological meaning to peaks

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Lesson https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-lesson How to add biological meaning to peaks Annotation, Chip-seq, Data Visualization, NGS
Chip-seq: Peak calling tutorial

The aim is to : Understand how to process reads to obtain peaks (peak-calling). Become familiar with differential analysis of peaks In practice : Obtain dataset from GEO Analyze mapped reads Obtain set(s) of peaks, handle replicates Differential analysis of peak

Keywords: Chip-seq, NGS, Peak calling

Chip-seq: Peak calling tutorial https://tess.elixir-europe.org/materials/chip-seq-peak-calling-tutorial The aim is to : Understand how to process reads to obtain peaks (peak-calling). Become familiar with differential analysis of peaks In practice : Obtain dataset from GEO Analyze mapped reads Obtain set(s) of peaks, handle replicates Differential analysis of peak Chip-seq, NGS, Peak calling
DNA - seq Bioinformatics Analysis

Detection of Copy Number Variations

Keywords: DNA-seq

DNA - seq Bioinformatics Analysis https://tess.elixir-europe.org/materials/dna-seq-bioinformatics-analysis Detection of Copy Number Variations DNA-seq
Third generation sequencing : the revolution of long reads

Introduction on sequencing: available technologies, library types, applications ...

Keywords: Genomics

Third generation sequencing : the revolution of long reads https://tess.elixir-europe.org/materials/third-generation-sequencing-the-revolution-of-long-reads Introduction on sequencing: available technologies, library types, applications ... Genomics
200 billion sequences and counting: analysis, discovery and exploration of datasets with EBI Metagenomics

EBI metagenomics (EMG, https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of...

Keywords: metagenomics

200 billion sequences and counting: analysis, discovery and exploration of datasets with EBI Metagenomics https://tess.elixir-europe.org/materials/200-billion-sequences-and-counting-analysis-discovery-and-exploration-of-datasets-with-ebi-metagenomics-ea1b32d5-b113-436c-a7da-8c7d29648d36 EBI metagenomics (EMG, https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA). EMG has recently undergone rapid expansion, with an over 10-fold increase in data volumes in the first 5 months of 2016. It now houses ~ 50k publicly available data sets, and represents one of the largest collections of analysed metagenomic data. As its data content has grown, EMG has increasingly become a platform for data discovery. To support this process, we have made a series of user-interface improvements, including the classification of projects by biome, presentation of results data for better visualisation and more convenient download, and provision of project level summary files. More recently, we have indexed project metadata for use with the EBI search engine, enabling exploration across different datasets. For example, users are able to search with a particular taxonomic lineage or protein function and discover the projects, samples and sequencing runs in which that lineage or function is found. This functionality allows users to explore associations between biomes, environmental conditions and organisms and functions (e.g., discovering protein coding sequences that correspond to certain enzyme families found in aquatic environments at a given temperature range). Here, we give an overview of the EMG data analysis pipeline and web site, and illustrate the use of the new search facility for data discovery. metagenomics 2016-12-16 2017-01-11
Connecting Galaxy to a compute cluster

Problems Running jobs on the Galaxy server negatively impacts Galaxy UI performance Even adding one other host helps Can restart Galaxy without interrupting jobs Solution: Connecter Galaxy to a computing cluster

Keywords: Cluster, Galaxy

Connecting Galaxy to a compute cluster https://tess.elixir-europe.org/materials/connecting-galaxy-to-a-compute-cluster Problems Running jobs on the Galaxy server negatively impacts Galaxy UI performance Even adding one other host helps Can restart Galaxy without interrupting jobs Solution: Connecter Galaxy to a computing cluster Cluster, Galaxy
From Samples to Data : Assuring Downstream Analysis with Upstream Planning

Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by...

Keywords: metagenomics

From Samples to Data : Assuring Downstream Analysis with Upstream Planning https://tess.elixir-europe.org/materials/from-samples-to-data-assuring-downstream-analysis-with-upstream-planning-6fac0f49-b453-4c15-a409-9753fb27ee9b Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by this powerful technology depends on sample preparation, library construction and the selection of appropriate sequencing technology and sequencing depth. Here we explore the different variables involved in the process of preparing samples for sequencing analysis including sample collection, DNA extraction and library construction. We also examine the various sequencing technologies deployed for routine metagenomic analysis and considerations for their use in different model systems including humans, mouse and the environment. Future developments such as long-reads will also be discussed to provide a complete picture of important aspects prior to data analyses which play a critical role in the success of metagenomic studies. metagenomics 2017-01-11
Variant annotation

Add meta-information on variant to facilitate interpretation

Keywords: Variant analysis

Variant annotation https://tess.elixir-europe.org/materials/variant-annotation Add meta-information on variant to facilitate interpretation Variant analysis
Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities

Meta3C is an experimental and computational approach that exploits the physical contacts experienced by DNA molecules sharing the same cellular compartments. These collisions provide a quantitativeinformation that allows interpreting and phasing the genomes present within complex mixes of species...

Keywords: metagenomics

Exploiting collisions between DNA molecules to characterize the genomic structures of complex communities https://tess.elixir-europe.org/materials/exploiting-collisions-between-dna-molecules-to-characterize-the-genomic-structures-of-complex-communities-e13ff1e3-f218-4367-b445-2a8e18bb7834 Meta3C is an experimental and computational approach that exploits the physical contacts experienced by DNA molecules sharing the same cellular compartments. These collisions provide a quantitativeinformation that allows interpreting and phasing the genomes present within complex mixes of species without prior knowledge. Not only the exploitation of chromosome physical 3D signatures hold interesting premises regarding solving the genome sequences from discrete species, but it also allows assigning mobile elements such as plasmids or phages to their hosts. metagenomics 2016-12-15 2017-01-11
Differential analysis of RNA-Seq data

Design, describe, explore and model

Keywords: Genomics, RNA-seq

Differential analysis of RNA-Seq data https://tess.elixir-europe.org/materials/differential-analysis-of-rna-seq-data Design, describe, explore and model Genomics, RNA-seq
Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification

PPF (Prokaryotic Phylogeny on the Fly) is an automated pipeline allowing to compute molecular phylogenies for prokarotic organisms. It is based on a set of specialized databases devoted to SSU rRNA, the most commonly used marker for bacterial txonomic identification. Those databases are splitted...

Keywords: metagenomics

Prokaryotic Phylogeny on the Fly: databases and tools for online taxonomic identification https://tess.elixir-europe.org/materials/prokaryotic-phylogeny-on-the-fly-databases-and-tools-for-online-taxonomic-identification-84732559-32a2-4c4c-9c94-2bd3c3773717 PPF (Prokaryotic Phylogeny on the Fly) is an automated pipeline allowing to compute molecular phylogenies for prokarotic organisms. It is based on a set of specialized databases devoted to SSU rRNA, the most commonly used marker for bacterial txonomic identification. Those databases are splitted into different subsets using phylogenetic information. The procedure for computing a phylogeny is completely automated. Homologous sequence are first recruited through a BLAST search performed on a sequence (or a set of sequences). Then the homologous sequences detected are aligned using one of the multiple sequence alignment programs provided in the pipeline (MAFFT, MUSCLE or CLUSTALO). The alignment is then filtered using BMGE and a Maximum Likelihood (ML) tree is computed using the program FastTree. The tree can be rooted with an outgroup provided by the user and its leaves are coloured with a scheme related to the taxonomy of the sequences. The main advantage provided by PPF is that its databases are generated using a phylogeny-oriented procedure and and therefore much more efficient for phylogentic analyses that "generic" collections such as SILVA (in the case SSU rRNA) por GenBank. It is therefore much more suited to compute prokaryotic molecular phylogenies than related systems such as the Phylogeny.fr online system. PPF can be accessed online at https://umr5558-bibiserv.univ-lyon1.fr/lebibi/PPF-in.cgi metagenomics 2016-12-16 2017-01-11
PASTEClassifier Tutorial

The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 )

Keywords: Genomics, Transposons

PASTEClassifier Tutorial https://tess.elixir-europe.org/materials/pasteclassifier-tutorial The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 ) Genomics, Transposons
Exploring microbiomes with the MicroScope Platform

This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational...

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics

Exploring microbiomes with the MicroScope Platform https://tess.elixir-europe.org/materials/exploring-microbiomes-with-the-microscope-platform This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational annotation of bacterial genomes: synteny Automatic functional assignation and expert annotation of genes Relational annotation of bacterial genomes: phylogenetic profiles Relational annotation of bacterial genomes: pan-genome analysis Relational annotation of bacterial genomes: metabolic pathways Syntactic re-annotation of public microbial genomes Syntactic annotation of microbial genomes Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics
Genomic copy number Tutorial

We will analyze the copy number variations of a human tumor (parotid gland carcinoma), limited to the chr17, from a WES (whole-exome sequencing) experiment. All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37).

Keywords: Copy number, Structural genomics

Genomic copy number Tutorial https://tess.elixir-europe.org/materials/genomic-copy-number-tutorial We will analyze the copy number variations of a human tumor (parotid gland carcinoma), limited to the chr17, from a WES (whole-exome sequencing) experiment. All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37). Copy number, Structural genomics
REPET: TEdenovo tutorial

The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE

Keywords: Annotation, Genomics

REPET: TEdenovo tutorial https://tess.elixir-europe.org/materials/repet-tedenovo-tutorial The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE Annotation, Genomics
RNA - Seq de novo

Practical session on transciptome de novo assembly

Keywords: RNA-seq

RNA - Seq de novo https://tess.elixir-europe.org/materials/rna-seq-de-novo Practical session on transciptome de novo assembly RNA-seq
Differential gene expression analysis : Practical part

RNA-seq: Differential gene expression analysis practical session

Keywords: Genomics, RNA-seq

Differential gene expression analysis : Practical part https://tess.elixir-europe.org/materials/differential-gene-expression-analysis-practical-part RNA-seq: Differential gene expression analysis practical session Genomics, RNA-seq
Chip-seq: Functional Annotation tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Chip-seq, Functional Annotation, NGS

Chip-seq: Functional Annotation tutorial https://tess.elixir-europe.org/materials/chip-seq-functional-annotation-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Chip-seq, Functional Annotation, NGS
Variants: alignment and pre-treatment; GATK

Variant calling practical session

Keywords: Genomics

Variants: alignment and pre-treatment; GATK https://tess.elixir-europe.org/materials/variants-alignment-and-pre-treatment-gatk-d2d0443e-60d2-48f0-bbec-53b94eb5b003 Variant calling practical session Genomics
A Quick and focused overview of R data types and ggplot2 syntax

R and RStudio overview.

Keywords: Graphical analysis, R, Statistics

A Quick and focused overview of R data types and ggplot2 syntax https://tess.elixir-europe.org/materials/a-quick-and-focused-overview-of-r-data-types-and-ggplot2-syntax-b0aa7b0d-f355-44d7-baed-93d124c0f3ba R and RStudio overview. Graphical analysis, R, Statistics
Training on Galaxy : Metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Training on Galaxy : Metagenomics https://tess.elixir-europe.org/materials/training-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
x2Go

Opening an x2go session to the IFBcloud

Keywords: Cloud

x2Go https://tess.elixir-europe.org/materials/x2go Opening an x2go session to the IFBcloud Cloud
Chip-seq Analysis

Quality, normalisation and peak calling

Keywords: Chip-seq, Genomics

Chip-seq Analysis https://tess.elixir-europe.org/materials/chip-seq-analysis Quality, normalisation and peak calling Chip-seq, Genomics
Galaxy Administration

How to use the administation panel of Galaxy

Keywords: Galaxy

Galaxy Administration https://tess.elixir-europe.org/materials/galaxy-administration How to use the administation panel of Galaxy Galaxy
Fast filtering, mapping and assembly of 16S ribosomal RNA

The application of next-generation sequencing technologies to RNA orDNA directly extracted from a community of organisms yields a mixtureof nucleotide fragments. The task to distinguish amongst these and tofurther categorize the families of ribosomal RNAs (or any other givenmarker) is an...

Keywords: metagenomics

Fast filtering, mapping and assembly of 16S ribosomal RNA https://tess.elixir-europe.org/materials/fast-filtering-mapping-and-assembly-of-16s-ribosomal-rna-83398e0f-76de-4945-b0a8-8274413a6a47 The application of next-generation sequencing technologies to RNA orDNA directly extracted from a community of organisms yields a mixtureof nucleotide fragments. The task to distinguish amongst these and tofurther categorize the families of ribosomal RNAs (or any other givenmarker) is an important step for examining the phylogeneticclassification of the constituting species. In thisperspective, we have developed a complete bioinformatics suite, called MATAM, capable of handling large sets of reads in a fast and accurate way. MATAM covers all steps of the analysis, from the identificationof reads of interest in the raw sequencing data to the reconstructionof the full-length sequences of the marker and alignment to areference database for taxonomic assignment. Part of MATAM is basedon the SortMeRNA software, also developed by the team. metagenomics 2016-12-16 2017-01-11
(Proxy) Web Server Choices and Configuration

Installation and configuration of NGiNX for Galaxy

Keywords: Galaxy, NGiNX

(Proxy) Web Server Choices and Configuration https://tess.elixir-europe.org/materials/proxy-web-server-choices-and-configuration Installation and configuration of NGiNX for Galaxy Galaxy, NGiNX
DNA-seq analysis: From raw reads to processed alignments

Objectives: Mapping the DNA-seq data to the reference genome Process the alignments for the variant calling

Keywords: Alignment, DNA-seq, Genomics, Variant calling

DNA-seq analysis: From raw reads to processed alignments https://tess.elixir-europe.org/materials/dna-seq-analysis-from-raw-reads-to-processed-alignments Objectives: Mapping the DNA-seq data to the reference genome Process the alignments for the variant calling Alignment, DNA-seq, Genomics, Variant calling
Users, Groups, and Quotas in Galaxy

How to handle Users, Groups, and Quotas in Galaxy

Keywords: Galaxy

Users, Groups, and Quotas in Galaxy https://tess.elixir-europe.org/materials/users-groups-and-quotas-in-galaxy How to handle Users, Groups, and Quotas in Galaxy Galaxy
Chip-seq: Introduction to the Workshop

Data visualization, quality control, normalization peak calling Peak annotation From peaks to motifs

Keywords: Chip-Seq

Chip-seq: Introduction to the Workshop https://tess.elixir-europe.org/materials/chip-seq-introduction-to-the-workshop Data visualization, quality control, normalization peak calling Peak annotation From peaks to motifs Chip-Seq
Docker and Galaxy

Questions Why Docker? What is it? How to use Docker? How to integrate Galaxy in Docker to facilitate its deployment? Objectives Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours

Keywords: Docker, Galaxy

Docker and Galaxy https://tess.elixir-europe.org/materials/docker-and-galaxy Questions Why Docker? What is it? How to use Docker? How to integrate Galaxy in Docker to facilitate its deployment? Objectives Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours Docker, Galaxy
MG-RAST — experiences from processing a quarter million metagenomic data sets

MG-RAST has been offering metagenomic analyses since 2007. Over 20,000 researchers have submitted data. I will describe the current MG-RAST implementation and demonstrate some of its capabilities. In the course of the presentation I will highlight several metagenomic pitfalls. MG-RAST:...

Keywords: metagenomics

MG-RAST — experiences from processing a quarter million metagenomic data sets https://tess.elixir-europe.org/materials/mg-rast-experiences-from-processing-a-quarter-million-metagenomic-data-sets-5c190d47-0371-4950-bee2-5ff5fccfc499 MG-RAST has been offering metagenomic analyses since 2007. Over 20,000 researchers have submitted data. I will describe the current MG-RAST implementation and demonstrate some of its capabilities. In the course of the presentation I will highlight several metagenomic pitfalls. MG-RAST: http://metagenomics.anl.gov MG-RAST-APP: http://api.metagenomics.anl.gov/api.html metagenomics 2016-12-16 2017-01-11
Chip-seq: Discovering motifs in peaks with RSAT

Read mapping: from raw reads to aligned reads. Peak calling: from aligned reads to regions/peaks of high read density. ChIP-seq annotation Identification of genes related to the peaks. Profiles of ChIP-seq reads around reference points (TSS, histone marks,). Functional enrichment of the...

Keywords: Chip Seq, Motif Analysis, NGS

Chip-seq: Discovering motifs in peaks with RSAT https://tess.elixir-europe.org/materials/chip-seq-discovering-motifs-in-peaks-with-rsat Read mapping: from raw reads to aligned reads. Peak calling: from aligned reads to regions/peaks of high read density. ChIP-seq annotation Identification of genes related to the peaks. Profiles of ChIP-seq reads around reference points (TSS, histone marks,). Functional enrichment of the genes related to the peaks. Chip Seq, Motif Analysis, NGS
The IFB cloud for bioinformatics

Practical work to introduce basic and advanced usage of the IFB cloud Howto launch virtual machines Managing your data in the cloud ; Howto to connect to your VMS (SSH, web, remote desktop) Personalizing your VMs (approver, galaxy, docker)

Keywords: Cloud computing, Virtual machine

The IFB cloud for bioinformatics https://tess.elixir-europe.org/materials/the-ifb-cloud-for-bioinformatics Practical work to introduce basic and advanced usage of the IFB cloud Howto launch virtual machines Managing your data in the cloud ; Howto to connect to your VMS (SSH, web, remote desktop) Personalizing your VMs (approver, galaxy, docker) Cloud computing, Virtual machine
Docker Tutorial

Docker is free software that automates the deployment of applications in software containers executant in isolation. A Docker container, away from traditional virtual machines, requires no separate operating system and not providing any but relies instead on the core functionality and uses the...

Keywords: Docker

Docker Tutorial https://tess.elixir-europe.org/materials/docker-tutorial Docker is free software that automates the deployment of applications in software containers executant in isolation. A Docker container, away from traditional virtual machines, requires no separate operating system and not providing any but relies instead on the core functionality and uses the isolation of resources and namespaces separated to isolate the operating system as seen by the application. Docker
Eukaryotic small RNA

Small RNAseq data analysis for miRNA identification

Keywords: RNA-seq

Eukaryotic small RNA https://tess.elixir-europe.org/materials/eukaryotic-small-rna Small RNAseq data analysis for miRNA identification RNA-seq
Chip Seq: Annotation and visualization Tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Annotation, Chip-seq, Data Visualization, NGS

Chip Seq: Annotation and visualization Tutorial https://tess.elixir-europe.org/materials/chip-seq-annotation-and-visualization-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Annotation, Chip-seq, Data Visualization, NGS
Welcome and Introduction

Introduction message of the EGDW 2017

Welcome and Introduction https://tess.elixir-europe.org/materials/welcome-and-introduction Introduction message of the EGDW 2017
Welcome message

Presentation of the workshop (Chairman: Claudine Médigue)

Keywords: metagenomics

Welcome message https://tess.elixir-europe.org/materials/welcome-message-69dc597e-f839-448f-9c9d-3622ddffd592 Presentation of the workshop (Chairman: Claudine Médigue) metagenomics 2016-12-15 2017-01-11
Statistics with RStudio

Introduction to statistics with R

Keywords: R

Statistics with RStudio https://tess.elixir-europe.org/materials/statistics-with-rstudio Introduction to statistics with R R
Galactic Database

How to choose a database for Galaxy and configure it

Keywords: Galaxy

Galactic Database https://tess.elixir-europe.org/materials/galactic-database How to choose a database for Galaxy and configure it Galaxy
Rationale and Tools to look for the unknown in (metagenomic) sequence data

The interpretation of metagenomic data (environmental, microbiome, etc, ...) usually involves the recognition of sequence similarity with previously identified (micro-organisms). This is for instance the main approach to taxonomical assignments and a starting point to most diversity analyses....

Keywords: metagenomics

Rationale and Tools to look for the unknown in (metagenomic) sequence data https://tess.elixir-europe.org/materials/rationale-and-tools-to-look-for-the-unknown-in-metagenomic-sequence-data-5dd1e1a8-6db2-4b78-b1fc-60e1a5fbcee8 The interpretation of metagenomic data (environmental, microbiome, etc, ...) usually involves the recognition of sequence similarity with previously identified (micro-organisms). This is for instance the main approach to taxonomical assignments and a starting point to most diversity analyses. When exploring beyond the frontier of known biology, one should expect a large proportion of environmental sequences not exhibiting any significant similarity with known organisms. Notably, this is the case for eukaryotic viruses belonging to new families, for which the proportion of "no match" could reach 90%. Most metagenomics studies tend to ignore this large fraction of sequences that might be the equivalent of "black matter" in Biology. We will present some of the ideas and tools we are using to extract that information from large metagenomics data sets in search of truly unknown microorganisms. One of the tools, "Seqtinizer", an interactive contig selection/inspection interface will also be presented in the context of "pseudo-metagenomic" projects, where the main organism under genomic study (such as sponges or corals) turns out to be (highly) mixed with an unexpected population of food, passing-by, or symbiotic microorganisms. metagenomics 2016-12-16 2017-01-11
Analysis of community composition data using phyloseq

Learn about and become familiar with phyloseq R package for the analysis of microbial census data

Keywords: Microbiomes, R

Analysis of community composition data using phyloseq https://tess.elixir-europe.org/materials/analysis-of-community-composition-data-using-phyloseq Learn about and become familiar with phyloseq R package for the analysis of microbial census data Microbiomes, R
Development in Galaxy

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.

Keywords: Galaxy

Development in Galaxy https://tess.elixir-europe.org/materials/development-in-galaxy Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project. Galaxy
Holistic metagenomics in marine communities

Complex microscopic communities are composed of species belonging to all life realms, from single-cell prokaryotes to multicellular eukaryotes of small size. Each component of a community needs to be studied for a full understanding of the functions performed by the whole assemblage, however...

Keywords: metagenomics

Holistic metagenomics in marine communities https://tess.elixir-europe.org/materials/holistic-metagenomics-in-marine-communities-62c31138-1982-4acd-9750-35dea2e77dc2 Complex microscopic communities are composed of species belonging to all life realms, from single-cell prokaryotes to multicellular eukaryotes of small size. Each component of a community needs to be studied for a full understanding of the functions performed by the whole assemblage, however methods to investigate microbiomes are generally restricted to a single kingdom. Using examples from the Tara Oceans project, we will show how size fractionation and use of varied metabarcoding, metagenomics and metatranscriptomics approaches can help studying the marine plankton community as a whole, in a wide geographic space. metagenomics 2016-12-16 2017-01-11
Snakemake tutorial: Gene regulation

Workflow 1: Rules and targets Workflow 2: Introducing wildcards Workflow 3: Keywords Workflow 4: Combining rules Workflow 5: Configuration file Workflow 6: Separated files

Keywords: Gene regulation, Snakemake

Snakemake tutorial: Gene regulation https://tess.elixir-europe.org/materials/snakemake-tutorial-gene-regulation-60b23a0f-6878-48bf-8ef0-f4e283f7ec03 Workflow 1: Rules and targets Workflow 2: Introducing wildcards Workflow 3: Keywords Workflow 4: Combining rules Workflow 5: Configuration file Workflow 6: Separated files Gene regulation, Snakemake
Searching for sequence: Tutorial

Quick Search is dedicated to a quick search for sequences or sequence families in the databases available on the PBIL server. It is an alternative to WWW Query which allows more complex queries. Quick Search allows you to retrieve sequences or sequence families associated to a single word without...

Keywords: genomics, pattern recognition

Searching for sequence: Tutorial https://tess.elixir-europe.org/materials/searching-for-sequence-tutorial Quick Search is dedicated to a quick search for sequences or sequence families in the databases available on the PBIL server. It is an alternative to WWW Query which allows more complex queries. Quick Search allows you to retrieve sequences or sequence families associated to a single word without specifying what is this word. You can enter indifferently a keyword, a sequence name or accession number, or a taxa name. genomics, pattern recognition
Galaxy: Initiation II

Galaxy II: common tools, quality control; alignment; data managment

Keywords: Genomics

Galaxy: Initiation II https://tess.elixir-europe.org/materials/galaxy-initiation-ii Galaxy II: common tools, quality control; alignment; data managment Genomics
A Simple Phylogenetic Tree Construction (part 1)

Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree. Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win).

Keywords: Phylogenetics

A Simple Phylogenetic Tree Construction (part 1) https://tess.elixir-europe.org/materials/a-simple-phylogenetic-tree-construction-part-1 Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree. Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win). Phylogenetics
Docker tutorial: Gene regulation

Get started with Docker! Create a Docker account Install Docker on your local host Create shared repositories and download source data Fetch the Docker image and run it with shared folders Execute the pipeline JVH / Mac

Keywords: Docker, Gene regulation

Docker tutorial: Gene regulation https://tess.elixir-europe.org/materials/docker-tutorial-gene-regulation Get started with Docker! Create a Docker account Install Docker on your local host Create shared repositories and download source data Fetch the Docker image and run it with shared folders Execute the pipeline JVH / Mac Docker, Gene regulation
Cross Taxa Tutorial

How query databases according to complex taxonomic critera Cross-Taxa allows to retrieve gene families that are shared by a given set of taxa, or which are specific to a set of taxa. It is also possible to select genes families which are associated to a certain set of taxa but which are not...

Keywords: genomics

Cross Taxa Tutorial https://tess.elixir-europe.org/materials/cross-taxa-tutorial How query databases according to complex taxonomic critera Cross-Taxa allows to retrieve gene families that are shared by a given set of taxa, or which are specific to a set of taxa. It is also possible to select genes families which are associated to a certain set of taxa but which are not found in a second set of taxa. Any taxonomic level can be used. genomics
Reconstructing genomes from metagenomes: The holy grail of microbiology

Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information...

Keywords: metagenomics

Reconstructing genomes from metagenomes: The holy grail of microbiology https://tess.elixir-europe.org/materials/reconstructing-genomes-from-metagenomes-the-holy-grail-of-microbiology-be78338f-13ef-40d6-92cf-621fbccf8808 Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information about the organization of genes in cognate genomes. Several factors affect the assembly performance, and the feasibility of the assembly-based approaches varies across environments. However, increasing read lengths, novel experimental approaches, advances in computational tools and resources, and improvements in assembly algorithms and pipelines render the assembly-based metagenomic workflow more and more accessible. The utility of metagenomic assembly remarkably increases when contigs are organized into metagenome-assembled genomes (MAGs). Often-novel MAGs frequently provide deeper insights into bacterial lifestyles that would otherwise remain unknown as evidenced by recent discoveries. The increasing rate of the recovery of MAGs presents new opportunities to link environmental distribution patterns of microbial populations and their functional potential, and transforms the field of microbiology by providing a more complete understanding of the microbial life, ecology, and evolution. metagenomics 2016-12-16 2017-01-11
Multiple Comparative Metagenomics using Multiset k-mer Counting

Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can...

Keywords: metagenomics

Multiple Comparative Metagenomics using Multiset k-mer Counting https://tess.elixir-europe.org/materials/multiple-comparative-metagenomics-using-multiset-k-mer-counting-4c0add23-9776-4d57-8bd2-43ce078fd286 Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the whole set of sequences, do not scale up on ambitious metagenomic projects. These limitations motivated the development of a new de novo metagenomic comparative method, called Simka. This method computes a large collection of standard ecology distances by replacing species counts by k-mer counts. Simka scales-up today metagenomic projects thanks to a new parallel k-mer counting strategy on multiple datasets. Experiments on public Human Microbiome Project datasets demonstrate that Simka captures the essential underlying biological structure. Simka was able to compute in a few hours both qualitative and quantitative ecology distances on hundreds of metagenomic samples (690 samples, 32 billions of reads). We also demonstrate that analyzing metagenomes at the k-mer level is highly correlated with extremely precise de novo comparison techniques which rely on all-versus-all sequences alignment strategy. metagenomics 2016-12-16 2017-01-11
Assessing microbial biogeography by using a metagenomic approach

Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors...

Keywords: metagenomics

Assessing microbial biogeography by using a metagenomic approach https://tess.elixir-europe.org/materials/assessing-microbial-biogeography-by-using-a-metagenomic-approach-2010019e-528d-4947-9056-e67e089ad240 Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors regulating the diversity of below-ground bacteria still need to be investigated, which limits our understanding of the distribution of such bacteria at various spatial scales. The overall objectives of this study were: (i) to determine the spatial patterning of bacterial community diversity in soils at a broad scale, and (ii) to rank the environmental filters most influencing this distribution. This study was performed at the scale of the France by using the French Soil Quality Monitoring Network. This network includes more than 2,200 soil samples along a systematic grid sampling. For each soil, bacterial diversity was characterized using a pyrosequencing approach targeting the 16S rRNA genes directly amplified from soil DNA, obtaining more than 18 million of high-quality sequences. This study provides the first estimates of microbial diversity at the scale of France, with for example, bacterial richness ranging from 555 to 2,007 OTUs (on average: 1,289 OTUs). It also provides the first extensive map of bacterial diversity, as well as of major bacterial taxa, revealing a bacterial heterogeneous and spatially structured distribution at the scale of France. The main factors driving bacterial community distribution are the soil physico-chemical properties (pH, texture...) and land use (forest, grassland, crop system...), evidencing that bacterial spatial distribution at a broad scale depends on local filters such as soil characteristics and land use when regarding the community (quality, composition) as a whole. Moreover, this study also offers a better evaluation of the impact of land uses on soil microbial diversity and taxa, with consequences in terms of sustainability for agricultural systems. metagenomics 2016-12-16 2017-01-11
ToolShed upload and tool-iuc PR

Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a...

Keywords: Galaxy

ToolShed upload and tool-iuc PR https://tess.elixir-europe.org/materials/toolshed-upload-and-tool-iuc-pr Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a Galaxy instance Be able to publish tools with Planemo Galaxy
Defining and importing genomes, Data Managers into Galaxy

Intro to built in datasets Built in data hierarchy Some problems Data Managers

Keywords: Galaxy

Defining and importing genomes, Data Managers into Galaxy https://tess.elixir-europe.org/materials/defining-and-importing-genomes-data-managers-into-galaxy Intro to built in datasets Built in data hierarchy Some problems Data Managers Galaxy
Galaxy Visualisation - Tutorial

Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in...

Keywords: Youri Hoogstrate

Galaxy Visualisation - Tutorial https://tess.elixir-europe.org/materials/galaxy-visualisation-tutorial Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in settings like zooming in and assigning colors, etc. Therefore, visualizations are ideally interactive, and changing settings is often an initial step in exploring data. For this reason it may be inconvenient to make use of static galaxy tools because it lacks these interactive features. For these situations Galaxy offers the option to create visualizations plugins, file format specific javascripts that integrate with the history menu, without making redundant copies of data. In this tutorial we shall go through how this system works and create a simple visualization plugin. The tool will create a visualization of the number of aligned reads per chromosome of a BAM file, and we will discuss possible optimizations and advantages and disadvantages of the proposed implementation. Youri Hoogstrate
Initiation to Galaxy

DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.

Keywords: DNA Analysis, Galaxy, Variant calling

Initiation to Galaxy https://tess.elixir-europe.org/materials/initiation-to-galaxy DNA-sequence analysis: from raw reads to variants calling within the galaxy environement. DNA Analysis, Galaxy, Variant calling
RNA-Seq: Differential Expression Analysis

Be careful about experimental design : avoid putting all the replicates in the same lane, using the same barcode for the replicates, putting different number of samples in lanes etc... Non- uniformity of the per base read distribution (Illumina Random Hexamer Priming bias visible on the 13...

Keywords: Differential Expression, RNA-seq, transcriptomics

RNA-Seq: Differential Expression Analysis https://tess.elixir-europe.org/materials/rna-seq-differential-expression-analysis Be careful about experimental design : avoid putting all the replicates in the same lane, using the same barcode for the replicates, putting different number of samples in lanes etc... Non- uniformity of the per base read distribution (Illumina Random Hexamer Priming bias visible on the 13 first bases) Bias hierarchy : biological condition concentration run/flowcell lane At equivalent expression level, a long gene will have more reads than a short one. Non random coverage along the transcript. Multiple hit for some reads alignments. Differential Expression, RNA-seq, transcriptomics
Sequencing 6000 chloroplast genomes : the PhyloAlps project

Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding...

Keywords: metagenomics

Sequencing 6000 chloroplast genomes : the PhyloAlps project https://tess.elixir-europe.org/materials/sequencing-6000-chloroplast-genomes-the-phyloalps-project-a2b30d75-061a-4663-a5b8-593842df23bf Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding initiative, phylogeneticists often prefer markers with better phylogenic properties, and ecologists, with the coming of the DNA metabarcoding, look for a third class of markers easiest to amplify from environmental DNA. Nevertheless they have all the same need of the knowledge accumulated by the others. But having different markers means that the sequecences have been got from different individuals in differente lab, following various protocoles. On that base, building a clean reference database, merging for each species all the available markers becomes a challenge. With the phyloAlps project we implement genome skimming at a large scale and propose it as a new way to set up such universal reference database usable by taxonomists, phylogeneticists, and ecologists. The Phyloalps project is producing for each species of the Alpine flora at least a genome skim composed of six millions of 100bp sequence reads. From such data it is simple to extract all chloroplastic, mitochondrial and nuclear rDNA markers commonely used. Moreover, most of the time we can get access to the complete chloroplast genome sequence and to a shallow sequencing of many nuclear genes. This methodes have already been successfully applied to algeae, insects and others animals. With the new single cell sequencing methods it will be applicable to most of the unicellular organisms. The good question is now : Can we consider the genome skimming as the next-generation DNA barcode ? metagenomics 2016-12-16 2017-01-11
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