maps short fixed-length polymorphic DNA sequence reads to reference sequences

 Maq (short for Mapping and Assembly with Quality) builds mapping assemblies
 from short reads generated by the next-generation sequencing machines. It was
 particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a
 preliminary functionality to handle ABI SOLiD data. Maq is previously known as
 mapass2.
 .
 Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.