Mapass2 is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, which typically generates reads 25-35bp in length. Mapass2 first aligns reads to reference sequences and then calls the consensus. At the mapping stage, maq performs ungapped alignment. For single-end reads, maq is able to find all hits with up to 2 or 3 mismatches, depending on a command-line option; for paired-end reads, it always finds all paired hits with one of the two reads containing up to 1 mismatch. At the assembling stage, maq calls the consensus based on a statistical model. It calls the base which maximizes the posterior probability and calculates a phred quality at each position along the consensus. Heterozygotes are also called in this process. For more information, see also maq website: http://mapass.sourceforge.net