MOSAIK: A hash-based algorithm for accurate next-generation sequencing read mapping

http://arxiv.org/pdf/1309.1149v1.pdf

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-net 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).