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Bug#489836: ITP: maq -- Mapping and Assembly with Quality

Package: wnpp
Severity: wishlist
Owner: Charles Plessy <plessy@debian.org>

  Package name    : maq
  Version         : 0.6.7
  Upstream Author : Heng Li <lh3@sanger.ac.uk>
  URL             : http://maq.sourceforge.net/
  License         : GPL-3
  Programming Lang: C
  Description     : Mapping and Assembly with Quality

 Maq builds mapping assemblies from short reads generated by the
 next-generation sequencing machines. It is particularly designed for
 Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to
 handle ABI SOLiD data. Maq is previously known as mapass2.
 With Maq you can:
  o     Fast align Illumina/SOLiD reads to the reference genome. With the
        default options, one million pairs of reads can be mapped to the
        human genome in about 10 CPU hours with less than 1G memory.
  o     Accurately measure the error probability of the alignment of each
        individual read.
  o     Call the consensus genotypes, including homozygous and heterozygous
        polymorphisms, with a Phred probabilistic quality assigned to each base.
  o     Find short indels with paired end reads.
  o     Accurately find large scale genomic deletions and translocations with
        paired end reads.
  o     Discover potential CNVs by checking read depth.
  o     Evaluate the accuracy of raw base qualities from sequencers and help
        to check the systematic errors.
 However, Maq can NOT:
  o     Do de novo assembly. (Maq can only call the consensus by mapping reads
        to a known reference.)
  o     Map shorts reads against themselves. (Maq can only find complete overlap
        between reads.)
  o     Align capillary reads or 454 reads to the reference. (Maq cannot align
        reads longer than 63bp.)

Like velvet and patman, this package is intended to be made available after
Lenny is released.

Preliminary packaging is available here:

Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/

Charles Plessy
Debian-Med packaging team.

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