Paketti: mapsembler2 (2.1.6+dfsg-1) [debports]

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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

Muut pakettiin mapsembler2 liittyvät paketit

• dep: bc

  GNU bc, rajattoman tarkka laskentakieli

• dep: libc6 (>= 2.4)

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6-udeb

• dep: libgcc2 (>= 4.2.1)

  Paketti ei saatavilla

• dep: libstdc++6 (>= 4.4.0)

  GNU standardi C++ -kirjasto, versio 3

• dep: zlib1g (>= 1:1.2.3.4)

  pakkauskirjaston ajonaikaistiedostot

Imuroi mapsembler2

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