Package: smalt
Version: 0.7.6-13
Architecture: riscv64
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 250
Depends: libbambamc0 (>= 0.0.50), libc6 (>= 2.34), zlib1g (>= 1:1.2.0.2)
Section: science
Priority: optional
Homepage: https://www.sanger.ac.uk/science/tools/smalt-0
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.
