Bug#737099: ITP: mapsembler2 -- bioinformatics targeted assembly software

[Olivier Sallou <olivier.sallou@irisa.fr>]

Package: wnpp
Severity: wishlist
Owner: Olivier Sallou <olivier.sallou@irisa.fr>

* Package name    : mapsembler2
  Version         : 2.0.5
  Upstream Author : INRIA
* URL             : https://colibread.inria.fr/mapsembler2/
* License         : CeCILL
  Programming Lang: C
  Description     : bioinformatics  targeted assembly software

Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler2 may be used for (not limited to):
· Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
· Checks if a gene (input as starter) has an homolog in a set of reads
· Checks if a known enzyme is present in a metagenomic NGS read set.
· Enrich unmappable reads by extending them, possibly making them mappable
· Checks what happens at the extremities of a contig
· Remove contaminants or symbiont reads from a read set