Maintainer: Debian Med Packaging Team <firstname.lastname@example.org>
Uploaders: Olivier Sallou <email@example.com>,
Andreas Tille <firstname.lastname@example.org>
Build-Depends: debhelper-compat (= 13),
Architecture: amd64 arm64 armel armhf hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 ppc64el s390x
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