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Source: smalt
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
zlib1g-dev,
python,
samtools,
libbambamc-dev
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/smalt
Vcs-Git: https://salsa.debian.org/med-team/smalt.git
Homepage: http://www.sanger.ac.uk/science/tools/smalt-0
Package: smalt
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Description: Sequence Mapping and Alignment Tool
SMALT efficiently aligns DNA sequencing reads with a reference genome.
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.
Package: smalt-examples
Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends}
Description: Sequence Mapping and Alignment Tool (examples)
SMALT efficiently aligns DNA sequencing reads with a reference genome.
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 contains example data and a test suite to test the data.
|
