Section: Software

Softwares for Next Generation Sequencing data

Participants : Dominique Lavenier [contact] , Pierre Peterlongo, Guillaume Rizk, Rayan Chikhi.

• GASSST: short reads mapper. See first section above.

• kisSnp and kisSplice : variant identification without the use of a reference genome. kisSnp is a tool to find single nucleotide polymorphisms (SNP) by comparing two sets of raw NGS reads. http://alcovna.genouest.org/kissnp/ KisSplice finds alternative splicings but also short insertions, deletions and duplications, SNPs and sequencing errors in one or two RNA-seq sets, without assembly nor mapping on a reference genome. http://alcovna.genouest.org/kissplice/

• Blastree: is a tool for computing intensive approximate pattern matching in a string graph. http://alcovna.genouest.org/blastree/

• Mapsembler: targeted assembly software. Mapsembler takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether the reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. http://alcovna.genouest.org/mapsembler/