BiRD develops data analysis pipelines with SnakeMake technology. This workflow development language is very efficient thanks to its fast and clear execution environment.

We are particularly working on developing reproducible pipelines. In the context of genomic data analysis, the same software components must be deployed in multiple environments for reproducibility, scalability and sharing issues.
To promote the principles of FAIR (Findable, Accessible, Interoperable, and Re-usable), the implementation of controlled software environments becomes mandatory. We seek to define good practices based on proven or promising tools: Git, Conda, SnakeMake, Jenkins and Docker.
These good development practices aim to promote data analysis pipelines accessible through web-based resources as well as pipelines that can be exchanged and re-run in the long term.

Shares

Our pipelines are hosted on our registery on GitLab@univ-nantes and registered on Biotools platform.

BiRD tools collection

Tool name     Description
 3SRP     A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis 
 microSysMics     This workflow provides an automated microbiome data analysis, starting with sequenced taxonomic markers (such as 16SrRNA) and using the standard QIIME2 toolbox to produce an abundance table and preliminary diversity, phylogeny and taxonomy analysis. 
 DEPIB     Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.