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Short description:
Please summarise the application in a few sentences. Avoid links here. 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.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Genomics, SNP detection,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Read mapping,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Command line,
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
Command-line tool,
The Wellcome Trust Sanger Institute
MAQ has been superseded by other, faster mapping programs, such as [[BWA]] by the same author.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.
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