[Debian-med-packaging] Bug#744960: ITP: smalt -- Sequence Mapping and Alignment Tool

[Andreas Tille]

Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille at debian.org>

* Package name    : smalt
  Version         : 0.7.6
  Upstream Author : Hannes Ponstingl <hp3 at sanger.ac.uk>
* URL             : http://www.sanger.ac.uk/resources/software/smalt/
* License         : GPL
  Programming Lang: C
  Description     : Sequence Mapping and Alignment Tool
 SMALT efficiently aligns DNA sequencing reads with a reference genome.
 It Reads from a wide range of sequencing platforms, for example Illumina,
 Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
 paired reads.
 .
 The software employs a perfect hash index of short words (< 20
 nucleotides long), sampled at equidistant steps along the genomic
 reference sequences.
 .
 For each read, potentially matching segments in the reference are
 identified from seed matches in the index and subsequently aligned with
 the read using a banded Smith-Waterman algorithm.
 .
 The best gapped alignments of each read is reported including a score
 for the reliability of the best mapping. The user can adjust the
 trade-off between sensitivity and speed by tuning the length and spacing
 of the hashed words.
 .
 A mode for the detection of split (chimeric) reads is provided.
 Multi-threaded program execution is supported.


This package is maintained by Debian Med team at
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/smalt/trunk/