BWA-SW
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Application data |
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| Created by | Heng Li and Richard Durbin |
|---|---|
| Biological application domain(s) | Mapping, Read alignment |
| Principal bioinformatics method(s) | FM-Index |
| Technology | Sanger, Illumina, 454 |
| Created at | Sanger Institute |
| Maintained? | Yes |
| Input format(s) | FASTQ, FASTA |
| Output format(s) | SAM |
| Software features | Gapped alignment, Local alignment |
| Programming language(s) | C |
| Licence | GPLv3, MIT License |
| Operating system(s) | UNIX |
Summary: Fast, accurate, memory-efficient aligner for long sequencing reads
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BWA-SW (Burrows-Wheeler Aligner, Smith-Waterman alignment) is an aligner that is distinct from BWA although it is included in the same downloadable package. It uses the same on-disk index as BWA, but the alignment algorithm is different. The BWA-SW algorithm is invoked by a BWA subcommand via bwa bwasw.
Features
BWA-SW
- computes local alignments (it finds alignments for parts of the input reads)
- works well on long reads
- is a bit slower than BWA
- does not support paired-end reads
- does not support colorspace reads
- helps to find chimeric reads: these are reads resulting from structural variations that map partially to one location on the reference and partially to a different location
Links
References
To add a reference for BWA-SW, enter the PubMed ID in the field below and click 'Add'.
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| Web Search | Wiki Sites | Scientific |
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