MAQ - Mapping and Assembly with Quality | Tool name | MAQ - Mapping and Assembly with Quality |
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| URL | http://maq.sourceforge.net |
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| Important features | 1. MAQ is used for aligning reads to reference sequences and then calls the consensus. It performs ungapped alignment.
2. It also performs assembly by calling the consensus based on a statistical model.
3. MAQ is used for SNP calling in the nucleotide space by converting color alignment to nucleotide alignment.
4. It does not consider the mapping quality of reads containing mutations, which will lead to high false negative rates due to the strategy used in calling SNPs.
5. It has two commands which will extract information from binary files:
a) cns2ref extracts the reference sequences from the consensus file.
b) cns2fq extracts the consensus sequences and their qualities. |
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| Citations | Li H, Ruan J, Durbin R.
Mapping short DNA sequencing reads and calling variants using mapping quality scores.
Genome Res. 2008 Nov;18(11):1851-8. Epub 2008 Aug 19.
PMID: 18714091 |
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| Year of publication | 2008 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | Alignment/Mapping, Reference assembler, SNP discovery |
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| Category | Free, Downloadable |
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| License | GNU GPL V3 |
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| Status | |
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| Input file format | FASTA, FASTQ |
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| Output file format | MAP, CNS, FASTA |
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| Operating system | Mac OS X, Linux |
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| Operating language | C, C++, Perl |
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| Platform | Illumina/Solexa, ABI SOLiD |
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| Maintained by | Wellcome Trust Sanger Institute
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| Downloadable file format | |
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| Submission file format | |
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