Section: New Software and Platforms


DISCOvering Single Nucleotide Polymorphism, Indels in RAD seq data

Keyword: RAD-seq

Functional Description: Software discoSnpRad is designed for discovering Single Nucleotide Polymorphism (SNP) and insertions/deletions (indels) from raw set(s) of RAD-seq data. Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed. The software is composed of several modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads2, enhances the kissnp2 results by computing per read set and for each variant found i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism. Then, variants are grouped by RAD locus, and a VCF file is finally generated. We also provide several scripts to further filter and select informative variants for downstream population genetics studies.

This tool relies on the GATB-Core library.

Release Functional Description: * Substantive improvements: better quality of results (accuracy and recall), better filtering of obtained results * Formal improvements: better organization of scripts, better presentation of results