Mapping short DNA sequencing reads and calling variants using mapping quality scores. Export

@article{li:maq, abstract = {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 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.}, address = {Sanger Institute;}, author = {Li, Heng and Ruan, Jue and Durbin, Richard}, citeulike-article-id = {3158518}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.078212.108}, citeulike-linkout-1 = {http://genome.cshlp.org/content/18/11/1851.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/18/11/1851.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18714091}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18714091}, day = {19}, doi = {10.1101/gr.078212.108}, issn = {1088-9051}, journal = {Genome research}, keywords = {dna, mapping, read, short}, month = {November}, number = {11}, pages = {1851--1858}, posted-at = {2008-10-31 14:13:24}, priority = {2}, title = {Mapping short DNA sequencing reads and calling variants using mapping quality scores.}, url = {http://dx.doi.org/10.1101/gr.078212.108}, volume = {18}, year = {2008} }

TY - JOUR ID - li:maq L3 - citeulike-article-id:3158518 N2 - 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 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. IS - 11 JF - Genome research SN - 1088-9051 AD - Sanger Institute; EP - 1858 TI - Mapping short DNA sequencing reads and calling variants using mapping quality scores. VL - 18 SP - 1851 KW - dna KW - mapping KW - read KW - short AU - Li, Heng AU - Ruan, Jue AU - Durbin, Richard PY - 2008/11/19/ UR - http://dx.doi.org/10.1101/gr.078212.108 ER -