MAQ specifications


Unique identifier OMICS_00668
Name MAQ
Alternative name Mapping and Assembly with Quality
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence, a reference sequence
Input format FASTA
Output data Consensus sequences and their qualities, list of SNPs, statistics about the coverage and SNPs
Output format fq, snp, log
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.5.0
Stability Stable
Maintained Yes


  • ill2sanger



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  • person_outline Richard Durbin <>

MAQ article

MAQ citations

PMCID: 5223720

[…] results and conclusions. maq-s, fb, sh, jt and pp designed the experiments/the study. maq-s, fb, sh, rs-q, ps, bc, jcm, el and pp analysed the data. maq-s, fb, jt and rsq collected the data. maq-s wrote the first draft of the paper. maq-s, sh, rs-q, fb, ps and pp contributed to the writing of the paper., funding: the study was funded by a grant from “vinci fondation vinci autoroutes pour […]

PMCID: 4359374

[…] deposited them under ncbi accessions numbers jn601139 and jq178331 respectively. illumina bodymap data were obtained from e-mtab-513., chip-seq and input reads from each species were aligned with maq (li et al., 2008) using default parameters to their respective genome assemblies (human [ncbi 36], macaque [mmul_1], mouse ncbi m37; rat [rgsc3.4] and dog [canfam2.0]). all sequence, genome […]

PMCID: 3960531

[…] package (cock et al., 2009) before assembly, excluding reads that would not properly pair, reads with ambiguous (‘n') base calls and reads with an average phred quality score below 20., we used maq v.0.7.1 (li et al., 2008) to align raw reads to atcc33209, the reference genome published in genbank ( ncbi accession number: nc_010168.1). maqs sol2sanger […]

PMCID: 2872544

[…] blood, primary tumor, metastasis, and xenograft were aligned to ncbi build36 using maq5 and coverage levels were defined by comparison of snps identified by illumina 1m duo arrays to snvs called by maq. somatic mutations were identified using our in-house programs glfsomatic and a modified version of the samtools indel caller ( putative variants were manually […]

PMCID: 2772860

[…] genotyping assay on an illumina® beadxpress with veracode™ technology. selection criteria for the snps were based on the illumine design score (above 0.8) and mac ranging from .5 to .15 detected by maq [19]. for the total 384 snps assayed, including 343 snps equally distributed along the chicken genome and 41 randomly selected snps that did not map to a single location in the chicken genome, […]

MAQ institution(s)
The Wellcome Trust Sanger Institute, Hinxton, UK; Beijing Genomics Institute, Chinese Academy of Science, Beijing, China
MAQ funding source(s)
This work was funded by the Wellcome Trust.

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