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maq

maps short fixed-length polymorphic DNA sequence reads to reference sequences

Variants:
Maq (short for Mapping and Assembly with Quality) 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: - 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. - Accurately measure the error probability of the alignment of each individual read. - Call the consensus genotypes, including homozygous and heterozygous polymorphisms, with a Phred probabilistic quality assigned to each base. - Find short indels with paired end reads. - Accurately find large scale genomic deletions and translocations with paired end reads. - Discover potential CNVs by checking read depth. - Evaluate the accuracy of raw base qualities from sequencers and help to check the systematic errors.

However, Maq can NOT: - Do de novo assembly. (Maq can only call the consensus by mapping reads to a known reference.) - Map shorts reads against themselves. (Maq can only find complete overlap between reads.) - Align capillary reads or 454 reads to the reference. (Maq cannot align reads longer than 63bp.)

This package is likely to be useful for users working with genetics or genomic studies in biology who need to assembly DNA sequences from fixed-length sequencers.

Homepage:
Package version:0.7.1-3
Architecture:mips
Distribution:Debian
Filename:maq_0.7.1-3_mips.deb

/usr/share/doc/maq/README

Mapass2 is a software that builds mapping assemblies from short reads
generated by the next-generation sequencing machines. It is particularly
designed for Illumina-Solexa 1G Genetic Analyzer, which typically
generates reads 25-35bp in length.

Mapass2 first aligns reads to reference sequences and then calls the
consensus. At the mapping stage, maq performs ungapped alignment.  For
single-end rea
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/usr/share/doc/maq/NEWS.gz

Beta Release 0.7.1 (26 September, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Version 0.7.0 does not work with reads >63bp at all. I overlooked two
lines of codes which assume reads are 63bp or shorter. Now I have fixed
the bug and tested it on simulated long reads. It seems to work fine. I
am sorry for this obvious bug. No other things are changed since 0.7.0.

(0.7.1: 26 September 2008, r672)
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/usr/share/man/man1/maq.1.gz

MAQ(1)                  Bioinformatics Tools                  MAQ(1)



NAME
       Maq - Mapping and Assembly with Qualities

SYNOPSIS
       maq command [options] arguments

       maq.pl command [options] arguments

DESCRIPTION
       Maq is a software that builds mapping assemblies from short
       reads generated by the next-generation sequencing machines.
       It is particularly designed 
more»

/usr/share/doc/maq/changelog.Debian.gz

maq (0.7.1-3) unstable; urgency=low

  * Distribute scripts that are not installed by upstream’s
 
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/usr/share/doc/maq/changelog.gz

------------------------------------------------------------------------
r666 | lh3lh3 | 2008-09-21 
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/usr/share/doc/maq/AUTHORS

Heng Li wrote all the codes of this project.


/usr/share/doc/maq/copyright

Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.

Name    :  Maq: Mappi
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