MAQ
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Application data |
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| Created by | Heng Li |
|---|---|
| Biological application domain(s) | Genomics, SNP detection |
| Principal bioinformatics method(s) | Read mapping |
| Created at | The Wellcome Trust Sanger Institute |
| Maintained? | No |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | Maq |
| Programming language(s) | C++, Perl |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | GPL |
Summary: Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.
"Error: no local variable "counter" was set." is not a number.
MAQ has been superseded by other, faster mapping programs, such as BWA by the same author. However, it's still good for some things (SNP calling mainly) and as it's primarily an alignment tool. It also comes with some useful PERL scripts for format conversion etc. MAQ does not align reads with indels.
MAQ's nonstandard output format can be converted to SAM format with tools included in the SAMtools distribution.
Links
References
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