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

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

What is Docker? Building an image BioShadock Orchestration

BioBlend module, a python library to use Galaxy API

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

Variant calling practical session

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...

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...

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...

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...

Visualisation of next-gen sequencing data with Integrative Genomics Viewer

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)

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...

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....

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

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

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...

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)....

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How to install a local instance of Galaxy

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

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...

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...

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...

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

Find Rapidly OTU with Galaxy Solution

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

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...

Detection of Copy Number Variations

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

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

Introduction to RADSeq through STACKS on Galaxy

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How to configure your local instance of Galaxy

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

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

How to add biological meaning to peaks

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

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

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...

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

Quality, normalisation and peak calling

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...

Variant calling practical session

Add meta-information on variant to facilitate interpretation

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 )

Design, describe, explore and model

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

How to use the administation panel of Galaxy

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).

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

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

Practical session on transciptome de novo assembly

RNA-seq: Differential gene expression analysis practical session

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

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...

How to choose a database for Galaxy and configure it

R and RStudio overview.

Find Rapidly OTU with Galaxy Solution

Opening an x2go session to the IFBcloud

Installation and configuration of NGiNX for Galaxy

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

How to handle Users, Groups, and Quotas in Galaxy

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

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

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)

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...

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...

Small RNAseq data analysis for miRNA identification

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

Introduction message of the EGDW 2017

Presentation of the workshop (Chairman: Claudine Médigue)

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...

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....

Introduction to statistics with R

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

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:...

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...

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...

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.

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...

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...

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

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

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...

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).

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

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...

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

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...

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...

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...

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...

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...

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...