Package: mapsembler2 (2.2.4+dfsg-3build2)

Links for mapsembler2

Trisquel Resources:

Download Source Package mapsembler2:

Maintainer:

Debian Med Packaging Team (Mail Archive)

Original Maintainers:

Debian Med Packaging Team (Mail Archive)
Olivier Sallou
Andreas Tille

External Resources:

Homepage [colibread.inria.fr]

Similar packages:

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

Other Packages Related to mapsembler2

depends

recommends

suggests

dep: bc

GNU bc arbitrary precision calculator language
dep: libc6 (>= 2.29)

GNU C Library: Shared libraries
also a virtual package provided by libc6-udeb
dep: libgcc-s1 (>= 3.0) [amd64]

GCC support library

dep: libgcc-s1 (>= 3.5) [armhf]
dep: libgomp1 (>= 4.9)

GCC OpenMP (GOMP) support library
dep: libstdc++6 (>= 5.2)

GNU Standard C++ Library v3
dep: zlib1g (>= 1:1.2.3.4)

compression library - runtime

Download mapsembler2

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Architecture	Package Size	Installed Size	Files
amd64	242.0 kB	791 kB	[list of files]
armhf	206.4 kB	487 kB	[list of files]

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