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BWA
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{{Bioinformatics application
|sw summary=Fast, accurate, memory-efficient aligner for short and long sequencing reads
|bio domain=Mapping, Read alignment|bio method=FM-IndexRead mapping,
|bio tech=Sanger, Illumina, 454, ABI SOLiD
|interface=Command line,
|created by=Heng Li and Richard Durbin
|created at=Sanger Institute
|sw feature=Gapped alignment, paired-end mapping
|language=C,
|licence=GPLv3, MIT License,
|os=UNIX,
}}
= Notes about the implementation Implementation notes =
The following notes were obtained by inspecting the source code. == 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."
* [http://sourceforge.net/mailarchive/message.php?msg_id=26175347 Solid paired-end patch] plus [http://sourceforge.net/mailarchive/message.php?msg_id=27685167 its correction]
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