Source: smalt Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 12), zlib1g-dev, python3, samtools, libbambamc-dev Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/smalt Vcs-Git: https://salsa.debian.org/med-team/smalt.git Homepage: https://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: ${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.