BWA
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Application data |
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| Created by | Heng Li and Richard Durbin |
|---|---|
| Biological application domain(s) | Read alignment, Mapping |
| Principal bioinformatics method(s) | FM-Index |
| Technology | Sanger, Illumina, 454, ABI SOLiD |
| Created at | Sanger Institute |
| Maintained? | Yes |
| Input format(s) | compressed/uncompressed fastq/fasta |
| Output format(s) | SAM |
| Software features | Gapped alignment, paired-end mapping |
| Programming language(s) | C |
| Licence | GPLv3, MIT |
| Operating system(s) | Unix |
Summary: Fast, accurate, memory-efficient aligner for short and long sequencing reads
"Error: no local variable "counter" was set." is not a number.
Links
- BWA Related [ edit link ]
- BWA Homepage [ edit link ]
References
To add a reference for BWA, enter the PubMed ID in the field below and click 'Add'.
Notes
Ambiguous bases in reference sequences
According to the BWA paper, "Non-A/C/G/T bases on the reference genome are converted to random nucleotides."
BWA uses a fixed seed for the random number generator. This means that running bwa index twice on the same FASTA file will result in the same index.
(The seed is set to 11 in bntseq.c.)
XT:A tag
N stands for for BWA_TYPE_NO_MATCH (bwtaln.h)
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