smalt - Sequence Mapping and Alignment Tool

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.



    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


    • /usr/bin/smalt
    • /usr/lib/smalt/test/sequenceReverseComplement_test
    • /usr/share/doc/smalt/changelog.Debian.gz
    • /usr/share/doc/smalt/copyright
    • /usr/share/man/man1/smalt.1.gz


    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)