Binary package “smalt” in ubuntu focal
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.
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The software employs a perfect hash index of short words (< 20
nucleotides long), sampled at equidistant steps along the genomic
reference sequences.
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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.
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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.
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A mode for the detection of split (chimeric) reads is provided.
Multi-threaded program execution is supported.
Source package
Published versions
- smalt 0.7.6-9 in amd64 (Proposed)
- smalt 0.7.6-9 in amd64 (Release)
- smalt 0.7.6-9 in arm64 (Proposed)
- smalt 0.7.6-9 in arm64 (Release)
- smalt 0.7.6-9 in armhf (Proposed)
- smalt 0.7.6-9 in armhf (Release)
- smalt 0.7.6-9 in ppc64el (Proposed)
- smalt 0.7.6-9 in ppc64el (Release)
- smalt 0.7.6-9 in riscv64 (Release)
- smalt 0.7.6-9 in s390x (Proposed)
- smalt 0.7.6-9 in s390x (Release)