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Mapping and Assembly with Quality MAQ

Builds mapping assemblies from short reads generated by the next-generation sequencing machines. Maq is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. Maq first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find all hits with up to 2 or 3 mismatches, depending on a command-line option; for paired-end reads, it always finds all paired hits with one of the two reads containing up to 1 mismatch. At the assembling stage, maq calls the consensus based on a statistical model.

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MAQ classification

MAQ specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTA
Output format:
fq, snp, log
Programming languages:
C, C++, Perl
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
A DNA sequence, a reference sequence
Output data:
Consensus sequences and their qualities, list of SNPs, statistics about the coverage and SNPs
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 3.0
Version:
0.5.0
Maintained:
Yes

MAQ distribution

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MAQ support

Documentation

Maintainer

  • Richard Durbin <>

Credits

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Publications

Institution(s)

The Wellcome Trust Sanger Institute, Hinxton, UK; Beijing Genomics Institute, Chinese Academy of Science, Beijing, China

Funding source(s)

This work was funded by the Wellcome Trust.

Link to literature

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