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About Us

Sigenae - an INRAE bioinformatic platform

Sigenae is an INRAE bioinformatic platform specialized in animal genomic data processing. Seven engineers located in Toulouse and Jouy-en-Josas help biologists to extract scientific knowledge from datasets generated by high-throughput sequencers and genotypers.

The team members co-authored numerous scientific publications.

Project support

The Sigenae team are involved in many projects.
See below, by topic, some examples of most significant supports.

Variant detection and annotation

Example with the 1000 goat genomes project - VarGoats...

De novo assembly and annotation of genomes

Example with the GenoFish project...

16S diversity

Example with metabarcoding analysis project - FROGS...

RNA-Seq transcriptomic analyses

Examples with recent projects...

System and software engineering

Example with Galaxy...

Trainings

The members of Sigenae are involved in numerous training courses...

Development project

The Sigenae team develops or is involved in the development of many tools, databases and workflows.
See below some examples of significant achievements.

  • All
  • Tools
  • Databases
  • Workflows

Web tool - Jvenn

Build venn diagram

Database - PhyloFish

Phylogenomic analysis of gene duplications in teleost fish: RNASeq approach

Tool - DRAP

De novo RNA-Seq Assembly Pipeline

Tool - Mintia

Metagenomic INserT BIoinformatic Annotation

Database - RumimiR

The bovine, caprine and ovine
miRNA database

Workflow snakemake

Variant calling

Database - NG6

A complete information system to process, store and download high-throughput sequencing data

Web tool - D-Genies

Dot plot large Genomes in an Interactive, Efficient and Simple way

Database - Public Sturgeon

The Public Sturgeon Transcripts Database

Tool - FROGS

Find, Rapidly, Otus with Galaxy Solution

Sigenae team

The members of the group are part of four INRAE divisions (GA, PHASE, MATHNUM and SA).

Christophe Klopp

Project coordinator

Genomic, Transcriptomic, Assembly
Data processing, AWK, Perl, Python, R.

Philippe Bardou

Bioinformatics engineer

DNAseq, Variant calling, sRNAseq (miRNA)
Perl, Python, GIT, HTML5, CSS3, Javascript.

Maria Bernard

Bioinformatics engineer

Variant calling, RADseq, Metagenomic, RNASeq, ASE
Python, Snakemake, GIT, Rmarkdown, Galaxy.

Cedric Cabau

Bioinformatics engineer

RNAseq, Assembly, Annotation
Perl, Awk, Python, GIT, HTML/CSS/JS.

Mathieu Charles

Bioinformatics engineer

Variant calling, CNV, RNAseq
Perl, Python, Java, C++, Snakemake, Jupyter, R.

Patrice Dehais

Sysadmin and B.E.

Sysadmin HPC Virtualization Parallelization/Optimization applied to bioinformatics software.

Cervin Guyomar

Bioinformatics engineer

Genomics, metagenomics, functional genomics
R, Python, NextFlow.

Sarah Maman

Bioinformatics engineer

RNAseq, Galaxy, elearning
Perl, Python, Cheetah, Nextflow.

Margot Zahm

Bioinformatics engineer

De novo genome assembly, Genome annotation
Python, Nextflow, R, GIT.

Frequently Asked Questions

  • Sigenae is a bioinformaticians team providing services to INRAE aquaculture and farm animal biologists.
    The Sigenae platform is part of the BioinfOmics Research Infrastructure of INRAE for bioinformatics.

  • Research teams of french research institutes: INRAE, CNRS, ENS, Ifremer, CIRAD, ENVT, Université de Perpignan. Among foreign parterns, we collaborate with researchers from the University of Würzburg (Germany), University of Montevideo (Uruguay), University of Szczecin (Poland), University of Lauzanne (Switzerland), Institute of Animal Reproduction and Food in Olsztyn (Poland), USDA Agricultural Research Service in Stoneville (USA), Leibniz-Institute of Freshwater Ecology and Inland Fisheries (Germany).

  • For any request please use this link to contact the Sigenae team.
    If you wish to contact any of us directly, please see the contact section below.

  • Depending on the help provided you can cite us in acknowledgements, references or both.

    Example for acknowledgements: we wish to thank the Sigenae group for ....

    Affiliations for references:

    C. Klopp, M. Zahm Sigenae, MIAT UR875, INRAE, F-31326, Castanet Tolosan, France.
    M. Bernard, M. Charles Sigenae, GABI, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
    P. Bardou, C. Cabau, P. Dehais, Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France.
    C. Guyomar, S. Maman

  • Just click on the thumbnails! Logos are available for dark or bright background.

Contact

The members of the group are located in two sites (Jouy-en-josas and Toulouse).
For any request please use this link to contact us.

Location:

Centre de recherche Occitanie-Toulouse
24, Chemin de Borde Rouge - Auzeville
CS 52627
31326 Castanet-Tolosan Cedex, FRANCE

First Name Last Name Phone Number
Christophe Klopp +335 61 28 50 36
Philippe Bardou +335 61 28 57 09
Cédric Cabau +335 61 28 54 60
Patrice Dehais +335 61 28 57 08
Cervin Guyomar +335 61 28 51 17
Sarah Maman +335 61 28 57 08
Margot Zahm +335 61 28 57 24

Location:

Centre INRAE de Jouy en Josas
Domaine de Vilvert
4 Avenue Jean Jaurès
F-78352 JOUY EN JOSAS Cedex, FRANCE

First Name Last Name Phone Number
Maria Bernard +331 34 65 25 77
Mathieu Charles +331 34 65 28 15