Package: mapsembler2 (2.2.4+dfsg1-4 and others)

Links for mapsembler2

Debian Resources:

Download Source Package mapsembler2:

Maintainers:

Debian Med Packaging Team (QA Page, Mail Archive)
Olivier Sallou (QA Page)
Andreas Tille (QA Page)
Étienne Mollier (QA Page)

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

enhances

dep: bc

GNU bc arbitrary precision calculator language
dep: libc6 (>= 2.11) [hppa]

GNU C Library: Shared libraries
also a virtual package provided by libc6-udeb

dep: libc6 (>= 2.16) [x32]

dep: libc6 (>= 2.17) [sh4]

dep: libc6 (>= 2.29) [amd64, arm64, ppc64el, s390x]

dep: libc6 (>= 2.4) [m68k, sparc64]

dep: libc6 (>= 2.8) [ppc64]
dep: libc6.1 (>= 2.8) [alpha]

GNU C Library: Shared libraries
also a virtual package provided by libc6.1-udeb
dep: libgcc-s1 (>= 3.0) [amd64, arm64, ppc64el, s390x]

GCC support library
dep: libgcc1 [x32]

Package not available

dep: libgcc1 (>= 1:4.1.1) [alpha, ppc64, sparc64]

dep: libgcc1 (>= 1:4.3) [sh4]
dep: libgcc2 (>= 4.2.1) [m68k]

Package not available
dep: libgcc4 (>= 4.1.1) [hppa]

Package not available
dep: libgomp1 (>= 4.9) [not m68k, sh4, sparc64]

GCC OpenMP (GOMP) support library
dep: libhdf5-7 [x32]

Package not available
dep: libhdf5-8 [alpha, hppa, ppc64]

Package not available
dep: libstdc++6 [x32]

GNU Standard C++ Library v3

dep: libstdc++6 (>= 4.4.0) [m68k, sh4, sparc64]

dep: libstdc++6 (>= 4.8) [hppa]

dep: libstdc++6 (>= 4.9) [alpha, ppc64]

dep: libstdc++6 (>= 5.2) [amd64, arm64, ppc64el, s390x]
dep: zlib1g (>= 1:1.2.3.4)

compression library - runtime

Download mapsembler2

Download for all available architectures
Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.2.3+dfsg-1	241.2 kB	910.0 kB	[list of files]
amd64	2.2.4+dfsg1-4	707.5 kB	1,283.0 kB	[list of files]
arm64	2.2.4+dfsg1-4	685.7 kB	1,247.0 kB	[list of files]
hppa (unofficial port)	2.2.3+dfsg-1	241.5 kB	803.0 kB	[list of files]
m68k (unofficial port)	2.1.6+dfsg-1	262.2 kB	453.0 kB	[list of files]
ppc64 (unofficial port)	2.2.3+dfsg-1	228.6 kB	928.0 kB	[list of files]
ppc64el	2.2.4+dfsg1-4	722.5 kB	1,571.0 kB	[list of files]
s390x	2.2.4+dfsg1-4	683.2 kB	1,307.0 kB	[list of files]
sh4 (unofficial port)	2.1.6+dfsg-1	285.5 kB	469.0 kB	[list of files]
sparc64 (unofficial port)	2.1.6+dfsg-1	263.1 kB	458.0 kB	[list of files]
x32 (unofficial port)	2.2.3+dfsg-1	233.7 kB	706.0 kB	[list of files]