MAQ

MAQ is a software tool used to align short reads to a reference genome and derive genotype calls of the consensus sequence of a diploid genome, such as in a human sample. The software is designed to use mate-pair information effectively and estimate the error probability of each read alignment. It is also capable of deriving error probabilities for the final genotype calls using a Bayesian statistical model that incorporates mapping qualities, error probabilities from raw sequence quality scores, sampling of the two haplotypes, and an empirical model for correlated errors at a site. MAQ is considered to be accurate, efficient, versatile, and user-friendly. However, its speed may be a concern when scaling up the alignment to the re-sequencing of hundreds of individuals.