smalt - Sequence Mapping and Alignment Tool

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name smalt
Package version 0.7.6
Package release 4
Package architecture i386
Package type deb
Installed size 342 B
Download size 116.31 KB
Official Mirror
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.


Package Version Architecture Repository
smalt_0.7.6-4_amd64.deb 0.7.6 amd64 Ubuntu Universe
smalt - - -


Name Value
libbambamc0 -
libc6 >= 2.7
zlib1g >= 1:


Type URL
Binary Package smalt_0.7.6-4_i386.deb
Source Package smalt

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install smalt deb package:
    # sudo apt-get install smalt




2014-10-14 - Andreas Tille <>
smalt (0.7.6-4) unstable; urgency=medium
* cme fix dpkg-control
* Use autotools-dev / since dh-autoreconf does not work this hopefully also 
Closes: #765256
2014-05-13 - Andreas Tille <>
smalt (0.7.6-3) unstable; urgency=medium
* Add missing "smalt" autopkgtest dependency (thanks to Martin
Pitt for the patch)
Closes: #747940
2014-04-25 - Andreas Tille <>
smalt (0.7.6-2) unstable; urgency=medium
* Deal with examples package only if arch=all is built
Closes: #745782
* Cleanup debian/rules from comments that became useless
2014-04-08 - Andreas Tille <>
smalt (0.7.6-1) unstable; urgency=low
* Initial release (Closes: #744960)

See Also

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