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Source: mapsembler2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
bc, zlib1g-dev, help2man
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mapsembler2/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mapsembler2/trunk/
Homepage: http://colibread.inria.fr/mapsembler2/
Package: mapsembler2
Architecture: any
Depends: ${misc:Depends}, ${shlibs:Depends},
zlib1g, bc
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
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