The DOI matches its Crossref record; 73 of the 73 references it cites were found in a registry or an index.
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
Open accessAbstract
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).
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationFast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Identification of common molecular subsequences
Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,940
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,486
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
SOAP2: an improved ultrafast tool for short read alignment
Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,760
Real-Time DNA Sequencing from Single Polymerase Molecules
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., et al. (2009) · Science · doi:10.1126/science.1162986 · Cited by 3,732
Cited by
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing
Kosugi, S., Momozawa, Y., Liu, X., Terao, C., Kubo, M., & Kamatani, Y. (2019) · Genome Biology · doi:10.1186/s13059-019-1720-5 · Cited by 508
Genome graphs and the evolution of genome inference
Paten, B., Novak, A. M., Eizenga, J. M., & Garrison, E. (2017) · Genome Research · doi:10.1101/gr.214155.116 · Cited by 351
Self-citationExtremely High Mutation Rate of HIV-1 In Vivo
Cuevas, J. M., Geller, R., Garijo, R., López-Aldeguer, J., & Sanjuán, R. (2015) · PLOS Biology · doi:10.1371/journal.pbio.1002251 · Cited by 371
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
Gardner, E. J., Lam, V. K., Harris, D. N., Chuang, N. T., Scott, E. C., Pittard, W. S., Mills, R. E., The 1000 Genomes Project Consortium, & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 367
Wampach, L., Heintz-Buschart, A., Fritz, J. V., Ramiro-Garcia, J., Habier, J., Herold, M., Narayanasamy, S., Kaysen, A., Hogan, A. H., Bindl, L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07631-x · Cited by 292
Metadata
- Authors
- Lee, W.-P., Stromberg, M. P., Ward, A., Stewart, C., Garrison, E. P., & Marth, G. T.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-03-05
- Volume
- 9
- Issue
- 3
- Pages
- e90581
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2021724381
- Cited by
- 279
- References
- 73
- FWCI
- 17.16
- Type
- journal article
- Language
- en
- Open access
- gold
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- Lee, W.-P., Stromberg, M. P., Ward, A., Stewart, C., Garrison, E. P., & Marth, G. T. (2014). MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. PLoS ONE. https://doi.org/10.1371/journal.pone.0090581
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