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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Institutions

SPS - Saclay Plant Sciences

Available tools

The SPS-Bioinformatics Analysis and Research Support (SPS-BARS) team has developed many tools in the framework of the SPS Bioanalysis open call.

All the tools are available for the SPS community, upon request at, on the sps-bioinfo gitlab : 

Here is the list of projects and their scientific coordinator:

BIOFERN: Bioinformatics pipeline for the transcriptomic comparison of two closely related species of fern
Coordinator: Sylvain MERLOT (
Tool: A nextflow pipeline for de novo transcriptome assembly using both long and short reads
Status: Tested and functional on the IPS2 cluster

COEXPRESS: Genes involved in aphid-host-bacteria interactions in a domestication context
Coordinator: Amandine CORNILLE (
Tool: A nextflow pipeline for RNA-seq data analysis from preprocessing to differential analysis
Status: Tested and functional on Genotoul cluster

ETARI : Expression Trajectories and Associated Regulatory Interactions
Coordinator: Olivier MARTIN (
Status: In progress

ImpFlow: Pipeline for high density genotype imputation in plants
Coordinator: Stéphane NICOLAS (
Tool: impflowR is an R package designed to generate simulated data to evaluate the quality of genotype imputation
Status: Tested and functional

ISOSEQ: Using long read sequencing for transcript annotation and alternative splicing analysis
Coordinator: Jérémie BAZIN (
Status: In progress

LeptAssemble: Leptosphaeria genome assembly
Coordinator: Nicolas LAPALU (
Tool: Snakemake pipeline to assemble and annotate highly compartmentalized fungal genomes
Status: Tested and functional on Genotoul cluster

MapRep: Mapping Modified Histones and Transcription Factors Binding Sites at Endogenous and Exogenous Repetitive DNA
Coordinator: Angélique DELERIS (
Tool: Snakemake pipeline used to identify plasmid insertions in a genome
Status: Tested and functional on IFB and Genotoul clusters

MetAnnotation: Improving the annotation of the plant specialized metabolome
Coordinator: François PERREAU (franç
Tool: R-shiny application to automate the search for duplicates, adducts, dimers, in-source fragmentation
Status: Tested and functional

methPLANT : Methylation data analysis pipeline
Coordinator: Nicolas BOUCHE (
Status: In progress

MSGenoVa : Development of a pipeline for detection and analysis of genomic variations from Illumina DNAseq sequencing
Coordinator: Françoise BUDAR (
Tool: Snakemeke pipeline for complete analysis of genomic variations in Illumina DNA libraries
Status: Tested and functional on IFB and Genotoul clusters

multiCRISPR: CRISPR multiplex genotyping by Pacbio sequencing
Coordinator: Jean-Denis FAURE (
Tool: A snakemake pipeline to genotype the Crispr-modified PCR amplicon sequenced with PacBio technology
Status: Tested and functional on Genotoul cluster

riboseq: Translational Control of plant stress response
Coordinator: Benoît CASTANDET (
Tool: A snakemake pipeline to analyze RIBO-seq and RNA-seq data and perform a combined differential analysis
Status: Tested and functional on the IPS2 cluster

SAPTICON: Stable Analytical PipelinesfortheTranscriptomes of Isolated Cells or Nuclei
Coordinator: Pierre HILSON (
Tool: A snakemake pipeline for RNA-seq data analysis to classify and compare cell populations.
Status: Beta

siPIPE: Small RNA library analysis pipeline to annotate small RNA clusters and identify their differential regulation
Coordinator: Thomas BLEIN (
Tool: A snakemake pipeline to study smallRNA accumulation clusters and perform differential analysis
Status: Tested and functional on IPS2, IFB and Genotoul clusters