smalt
Sequence Mapping and Alignment Tool
Command lineScience
Not tested on a device yet. What that means
Commands in the package
smalt
About smalt
From Debian's package description
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.
From Debian's description of the smalt package, under that package's license.
Dependencies
Depends on
libbambamc0libc6zlib1g
Related apps
- muscleMultiple alignment program of protein sequencesCommand line
- clustaloGeneral-purpose multiple sequence alignment program for proteinsCommand line
- mafftMultiple alignment program for amino acid or nucleotide sequencesCommand line
- kalignGlobal and progressive multiple sequence alignmentCommand line
- probconsPROBabilistic CONSistency-based multiple sequence alignmentCommand line
- prodamultiple alignment of protein sequencesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the smalt package, under that package's license.
- Description: Debian's description of the smalt package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.