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Merge branch 'dev'

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Heng Li 2014-11-19 09:37:10 -05:00
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@ -32,6 +32,11 @@ SourceForge. After you acquire the source code, simply use `make` to compile
and copy the single executable `bwa` to the destination you want. The only and copy the single executable `bwa` to the destination you want. The only
dependency required to build BWA is [zlib][14]. dependency required to build BWA is [zlib][14].
Since 0.7.11, precompiled binary for x86\_64-linux is available in [bwakit][17].
In addition to BWA, this self-consistent package also comes with bwa-associated
and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs,
adapter triming, duplicate marking, HLA typing and associated data files.
##Seeking helps ##Seeking helps
The detailed usage is described in the man page available together with the The detailed usage is described in the man page available together with the
@ -146,3 +151,4 @@ as well. BWA-MEM does not have this problem.
[14]: http://zlib.net/ [14]: http://zlib.net/
[15]: https://github.com/lh3/bwa/tree/mem [15]: https://github.com/lh3/bwa/tree/mem
[16]: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/ [16]: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/
[17]: http://sourceforge.net/projects/bio-bwa/files/bwakit/