Bug#744960: ITP: smalt -- Sequence Mapping and Alignment Tool
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : smalt
Version : 0.7.6
Upstream Author : Hannes Ponstingl <hp3@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/
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