title: MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
abstract: MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.
authors.forename: Wan-Ping
authors.initials: WP
authors.lastname: Lee
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Stromberg
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.
authors.forename: Alistair
authors.initials: A
authors.lastname: Ward
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
authors.forename: Chip
authors.initials: C
authors.lastname: Stewart
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.
authors.forename: Erik P
authors.initials: EP
authors.lastname: Garrison
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.
authors.forename: Gabor T
authors.initials: GT
authors.lastname: Marth
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods; D004926:Escherichia coli / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D020071:Interspersed Repetitive Sequences; D016571:Neural Networks, Computer; D020641:Polymorphism, Single Nucleotide; D012372:ROC Curve; D017422:Sequence Analysis, DNA; D012984:Software