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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 SPS-Bioinfo@inrae.fr, on the sps-bioinfo gitlab : https://forgemia.inra.fr/sps-bioinfo 

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 (sylvain.merlot@i2bc.paris-saclay.fr)
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 (amandine.cornille@inrae.fr)
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 (olivier.c.martin@inrae.fr)
Status: In progress

ImpFlow: Pipeline for high density genotype imputation in plants
Coordinator: Stéphane NICOLAS (stephane.nicolas@inrae.fr)
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 (jeremie.bazin@universite-paris-saclay.fr)
Status: In progress

LeptAssemble: Leptosphaeria genome assembly
Coordinator: Nicolas LAPALU (nicolas.lapalu@inrae.fr)
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 (angelique.deleris@i2bc.paris-saclay.fr)
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 (françois.perreau@inrae.fr)
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 (nicolas.bouche@inrae.fr)
Status: In progress

MSGenoVa : Development of a pipeline for detection and analysis of genomic variations from Illumina DNAseq sequencing
Coordinator: Françoise BUDAR (francoise.budar@inrae.fr)
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 (Jean-Denis.Faure@inrae.fr)
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 (benoit.castandet@ips2.universite-paris-saclay.fr)
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 (Pierre.Hilson@inrae.fr)
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 (thomas.blein@cnrs.fr)
Tool: A snakemake pipeline to study smallRNA accumulation clusters and perform differential analysis
Status: Tested and functional on IPS2, IFB and Genotoul clusters