MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

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 4...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Wan-Ping Lee, Michael P Stromberg, Alistair Ward, Chip Stewart, Erik P Garrison, Gabor T Marth
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/adf62c12502548b7afdddbe7d83ada01
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:adf62c12502548b7afdddbe7d83ada01
record_format	dspace
spelling	oai:doaj.org-article:adf62c12502548b7afdddbe7d83ada012021-11-18T08:29:33ZMOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.1932-620310.1371/journal.pone.0090581https://doaj.org/article/adf62c12502548b7afdddbe7d83ada012014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24599324/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203MOSAIK 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).Wan-Ping LeeMichael P StrombergAlistair WardChip StewartErik P GarrisonGabor T MarthPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e90581 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wan-Ping Lee Michael P Stromberg Alistair Ward Chip Stewart Erik P Garrison Gabor T Marth MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
description	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).
format	article
author	Wan-Ping Lee Michael P Stromberg Alistair Ward Chip Stewart Erik P Garrison Gabor T Marth
author_facet	Wan-Ping Lee Michael P Stromberg Alistair Ward Chip Stewart Erik P Garrison Gabor T Marth
author_sort	Wan-Ping Lee
title	MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
title_short	MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
title_full	MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
title_fullStr	MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
title_full_unstemmed	MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
title_sort	mosaik: a hash-based algorithm for accurate next-generation sequencing short-read mapping.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/adf62c12502548b7afdddbe7d83ada01
work_keys_str_mv	AT wanpinglee mosaikahashbasedalgorithmforaccuratenextgenerationsequencingshortreadmapping AT michaelpstromberg mosaikahashbasedalgorithmforaccuratenextgenerationsequencingshortreadmapping AT alistairward mosaikahashbasedalgorithmforaccuratenextgenerationsequencingshortreadmapping AT chipstewart mosaikahashbasedalgorithmforaccuratenextgenerationsequencingshortreadmapping AT erikpgarrison mosaikahashbasedalgorithmforaccuratenextgenerationsequencingshortreadmapping AT gabortmarth mosaikahashbasedalgorithmforaccuratenextgenerationsequencingshortreadmapping
_version_	1718421762074476544

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

Ejemplares similares