MAQ protocols

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


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  • person_outline Richard Durbin <>

Publication for Mapping and Assembly with Quality

MAQ IN pipelines

PMCID: 4065252
PMID: 24717808
DOI: 10.1534/g3.114.011312

[…] (trapnell et al. 2012) was used to generate scatter plots and volcano plots. functional enrichment of sets of genes was assessed with funcat (ruepp et al. 2004) or blast2go (conesa et al. 2005)., maq (li et al. 2008) was used to map rna sequencing (rna-seq) reads to the genome sequence of n. crassa strain fgsc 2489 (galagan et al. 2003) and for the identification of single nucleotide […]

PMCID: 4359374
PMID: 25279814
DOI: 10.7554/eLife.02626.031

[…] 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: 3772057
PMID: 24068945
DOI: 10.1371/journal.pgen.1003723

[…] sequenced with 36 cycles on an illumina genome analyzer ii. each sample pool was sequenced using a single lane of illumina gaii analyzer flowcell; 36-base pair reads were aligned to the genome using maq algorithm [37] and base qualities were recalibrated using gatk (genome analysis toolkit) [38]. finally, variant discovery was performed using the previously described syzygy software, designed […]

PMCID: 3422356
PMID: 22912734
DOI: 10.1371/journal.pone.0042758

[…] sequences had been identified among the contigs, complete sequences of the most similar viruses were retrieved from sequence databases and used as references for alignment of small-rna reads with maq (maq user's manual, release 0.5.0) as in previous studies [12], [21] and also novoalign. the programs are similar, but novoalign optimizes the algorithm to produce a more accurate alignment […]

PMCID: 3428670
PMID: 22583744
DOI: 10.1186/1471-2164-13-183

[…] after this more stringent filtering step, we were left with a total 823.7 mbp of unique sequence, with 6,905 unmapped contigs., reads were aligned to the masked and filtered reference genome using maq [40]. we allowed some mismatches in the alignment process to account for sequence divergence between white leghorn and red junglefowl [41]. alignment results were summarized for each contig using […]

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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