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bwa

Burrows-Wheeler Aligner

Variants:
Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200 bp and the latter for longer sequences up to around 100 kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.
Homepage:
Package version:0.5.8c-1
Architecture:amd64
Distribution:Debian
Filename:bwa_0.5.8c-1_amd64.deb

/usr/share/doc/bwa/NEWS.gz

Beta Release 0.5.8 (8 June, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in bwasw:

 * Fixed an issue of missing alignments. This should happen rarely and
   only when the contig/read alignment is multi-part. Very rarely, bwasw
   may still miss a segment in a multi-part alignment. This is difficult
   to fix, although possible.

Notable changes in bwa-short:

 * Discard the SW alignme
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/usr/share/man/man1/bwa.1.gz

bwa(1)                  Bioinformatics tools                  bwa(1)



NAME
       bwa - Burrows-Wheeler Alignment Tool

SYNOPSIS
       bwa index -a bwtsw database.fasta

       bwa aln database.fasta short_read.fastq > aln_sa.sai

       bwa   samse   database.fasta  aln_sa.sai  short_read.fastq  >
       aln.sam

       bwa sampe  database.fasta  aln_sa1.sai  aln_sa2.sai  read1.fq
       read2
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/usr/share/doc/bwa/changelog.Debian.gz

bwa (0.5.8c-1) unstable; urgency=low

  * Bug fix release, reverting the scoring system back to the one used in
    0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not
    happen in principle. Such wrong cigars also incur errors in indel calling
    when samtools is in use (Closes: #601568).
  * Incremented Standards-Version to reflect conformance with Policy 3.9.1
    (debian/c
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/usr/share/doc/bwa/changelog.gz

------------------------------------------------------------------------
r1536 | lh3 | 2010-10-16 23
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/usr/share/doc/bwa/copyright

Format: DEP-5 (beta)
Source: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.8c.tar.bz2
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