软件包：smalt（0.7.6-13）
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.
其他与 smalt 有关的软件包
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- dep: libbambamc0 (>= 0.0.50)
- Runtime library for reading and writing BAM (genome alignment) files
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- dep: libc6 (>= 2.34)
- GNU C 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6-udeb
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- dep: zlib1g (>= 1:1.2.0.2)
- 压缩库 - 运行时