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 30 materials out of 97. View all results.

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). We will analyze the copy number...

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). 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

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

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. 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

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 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

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

Find Rapidly OTU with Galaxy Solution 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 Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics

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. 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

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

Introduction to RADSeq through STACKS on Galaxy 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 Introduction to RADSeq through STACKS on Galaxy NGS

Detection of Copy Number Variations 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 Detection of Copy Number Variations DNA-seq

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) Practical work to introduce basic...

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) 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

No description available 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 No description available Copy number, Structural genomics

Visualisation of next-gen sequencing data with Integrative Genomics Viewer 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 Visualisation of next-gen sequencing data with Integrative Genomics Viewer Data visualization, Genomics, NGS

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

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

How to install a local instance of Galaxy 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 How to install a local instance of Galaxy Galaxy

Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools 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 Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools Genomics, NGS, RNA-seq, SNP, Transcriptomics

Not available 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 Not available RNA-seq

Quality, normalisation and peak calling 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 Quality, normalisation and peak calling Chip-seq, Genomics

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 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

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. 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

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. 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

Small RNAseq data analysis for miRNA identification 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 Small RNAseq data analysis for miRNA identification RNA-seq

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. 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

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. 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

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 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

Transcriptome analysis provides information about the identity and quantity of all RNA molecules 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 Transcriptome analysis provides information about the identity and quantity of all RNA molecules Genomics, RNA-seq

Not available Not available

Keywords: Transcriptomics

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

How to use the administation panel of Galaxy 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 How to use the administation panel of Galaxy Galaxy

Galaxy II: common tools, quality control; alignment; data managment 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 Galaxy II: common tools, quality control; alignment; data managment Genomics
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  • 7ème école de bioinformatique AVIESAN-IFB

    25 - 30 November 2018

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    7ème école de bioinformatique AVIESAN-IFB https://tess.elixir-europe.org/events/7eme-ecole-de-bioinformatique-aviesan-ifb Initiation au traitement des données de génomique obtenues par séquençage à haut débit 2018-11-25 09:00:00 UTC 2018-11-30 00:00:00 UTC Roscoff Roscoff [] [] [] [] []
  • Ecole thématique CNRS 2018

    17 - 22 June 2018

    Elixir node event
    Ecole thématique CNRS 2018 https://tess.elixir-europe.org/events/ecole-thematique-cnrs-2018 Transcriptomique et épigénomique en cellule unique: théorie et pratique (sincellTE) 2018-06-17 09:00:00 UTC 2018-06-22 00:00:00 UTC Station Biologique Roscoff Station Biologique Roscoff [] [] [] [] []
  • analyse de données metabarcoding

    13 - 17 May 2018

    Elixir node event
    analyse de données metabarcoding https://tess.elixir-europe.org/events/analyse-de-donnees-metabarcoding introduire les concepts clés liés aux analyses de metabarcoding et les illustrer au moyen de cas concrets d’analyse 2018-05-13 09:00:00 UTC 2018-05-17 00:00:00 UTC ROSCOFF ROSCOFF [] [] [] [] []
  • RNAseq de novo assembly - Genotoul (second session)

    5 June 2018

    Elixir node event
    RNAseq de novo assembly - Genotoul (second session) https://tess.elixir-europe.org/events/rnaseq-de-novo-assembly-genotoul-second-session Training course for bio-informaticians and biologists aiming at introduce analysis of sequences 2018-06-05 09:00:00 UTC 2018-06-05 00:00:00 UTC Inra, 24 ch. de Borderouge, Auzeville Inra, 24 ch. de Borderouge, Auzeville [] [] [] [] []
  • MicroScope Open Days

    14 - 15 May 2018

    Elixir node event
    MicroScope Open Days https://tess.elixir-europe.org/events/microscope-open-days Journées utilisateurs de la plateforme MicroScope. 2018-05-14 09:00:00 UTC 2018-05-15 00:00:00 UTC Institut Pasteur Paris Institut Pasteur Paris [] [] [] [] []
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