Section: Software and Platforms

Next Generation Sequencing

Participants : Alexan Andrieux, Dominique Lavenier, Claire Lemaitre, Nicolas Maillet, Pierre Peterlongo, Guillaume Rizk, Erwan Drezen, Charles Deltel.

• Genome assembly [contact: P. Peterlongo]

  • Minia : ultra low memory footprint assembly Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet). http://minia.genouest.org/

  • Mapsembler: targeted assembly software. Mapsembler is a targeted assembly software. From sets of NGS raw reads and a set of input sequences (starters), it determines if each starter could be constructed from the reads. 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://colibread.inria.fr/mapsembler2/

  • Bloocoo: memory-efficient read correction Bloocoo is a software to identify sequencing errors in short-read datasets and correct them. It is based on an efficient data structure that enables to keep a very low memory footprint. http://gatb.inria.fr

• Variant detection [contact: C. Lemaitre]

  • discoSnp and kisSplice : variant identification without the use of a reference genome. discoSnp is a tool to find single nucleotide polymorphisms (SNP) by comparing two sets of raw NGS reads. http://colibread.inria.fr/discosnp/ 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://colibread.inria.fr/software/kissplice/

  • Kissreads: quantification of variants Kissreads considers sets of NGS raw reads and a set of input sequences (starters). Mapping reads to each starter, it provides quantitative (coverage depth) and qualitative (mapped read quality) information about each starter.

  • MindTheGap : detection of large insertions MindTheGap is a tool to detect large insertion events in re-sequencing data with respect to a reference genome. http://gatb.inria.fr

• Read mapping [contact: D. Lavenier]

  • GASSST: short reads mapper The GASSST software (Global Alignment Short Sequence Search Tool) is a general purpose mapper. GASSST finds global alignments of short DNA sequences against large DNA banks. One main characteristic of GASSST is its ability to perform fast gapped alignments and to process long reads compared to other current similar tools. http://www.irisa.fr/symbiose/projects/gassst/