Changes

|sw 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. Written by Heng Li from the Sanger Centre.|bio domain=Genomics, SNP discoverydetection,|bio method=MappingRead mapping,|interface=Command line, |resource type=Command-line tool,

MAQ has been superseded by other, faster mapping programs, such as [[BWA]] by the same author.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 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.