all options
buster  ] [  bullseye  ] [  bookworm  ] [  trixie  ] [  sid  ]
[ Source: smalt  ]

Package: smalt (0.7.6-12)

Links for smalt

Screenshot

Debian Resources:

Download Source Package smalt:

Maintainers:

External Resources:

Similar packages:

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.

Other Packages Related to smalt

  • depends
  • recommends
  • suggests
  • enhances

Download smalt

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 112.0 kB307.0 kB [list of files]
arm64 101.9 kB287.0 kB [list of files]
armel 97.1 kB273.0 kB [list of files]
armhf 96.1 kB197.0 kB [list of files]
i386 124.0 kB345.0 kB [list of files]
mips64el 106.7 kB343.0 kB [list of files]
mipsel 112.7 kB341.0 kB [list of files]
ppc64el 124.1 kB407.0 kB [list of files]
s390x 105.0 kB319.0 kB [list of files]