Michael Eisen's Group at UC Berkeley http://www.citeulike.org/groupfunc/652 CiteULike.org en-gb Copyright © 2004-2007 Oversity Limited http://www.citeulike.org/group/652/article/3177508 New sequencing technologies promise a new era in the use of DNA sequence. However, some of these technologies produce very short reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software. In particular, there is a major issue in efficiently aligning short reads to a reference genome, and handling ambiguity or lack of accuracy in this alignment. Here we introduce the concept of mapping quality, a measure of the confidence that a read actually comes from the position it is aligned to by the mapping algorithm. We describe the software MAQ that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g. from a human sample. MAQ makes full use of mate-pair information and accurately estimates the error probability of each read alignment. Error probabilities are also derived for the final genotype calls, using a Bayesian statistical model that incorporates the mapping qualities, error probabilities from the raw sequence quality scores, sampling of the two haplotypes, and an empirical model for correlated errors at a site. Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile and user friendly. It is freely available at http://maq.sourceforge.net. 2008-09-01T05:21:33+00:00 http://www.citeulike.org/profile/orzenil 2008-08-17T18:19:31+00:00