CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.

The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Mo...

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Autores principales:	Yongchao Liu, Bernt Popp, Bertil Schmidt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/607ddbc33c7f428aaefb6bdec3db870f
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id	oai:doaj.org-article:607ddbc33c7f428aaefb6bdec3db870f
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spelling	oai:doaj.org-article:607ddbc33c7f428aaefb6bdec3db870f2021-11-18T08:36:19ZCUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.1932-620310.1371/journal.pone.0086869https://doaj.org/article/607ddbc33c7f428aaefb6bdec3db870f2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24466273/?tool=EBIhttps://doaj.org/toc/1932-6203The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorporates three different seed types, i.e. maximal exact match seeds, exact-match k-mer seeds and variable-length seeds, into the alignment pipeline. Furthermore, three techniques: weighted seed-pairing heuristic, paired-end alignment pair ranking and read mate rescuing have been conceived to facilitate accurate paired-end alignment. For base-space alignment, we have compared CUSHAW3 to Novoalign, CUSHAW2, BWA-MEM, Bowtie2 and GEM, by aligning both simulated and real reads to the human genome. The results show that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novoalign for short-reads with high error rates. For color-space alignment, CUSHAW3 is consistently one of the best aligners compared to SHRiMP2 and BFAST. The source code of CUSHAW3 and all simulated data are available at http://cushaw3.sourceforge.net.Yongchao LiuBernt PoppBertil SchmidtPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e86869 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yongchao Liu Bernt Popp Bertil Schmidt CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
description	The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorporates three different seed types, i.e. maximal exact match seeds, exact-match k-mer seeds and variable-length seeds, into the alignment pipeline. Furthermore, three techniques: weighted seed-pairing heuristic, paired-end alignment pair ranking and read mate rescuing have been conceived to facilitate accurate paired-end alignment. For base-space alignment, we have compared CUSHAW3 to Novoalign, CUSHAW2, BWA-MEM, Bowtie2 and GEM, by aligning both simulated and real reads to the human genome. The results show that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novoalign for short-reads with high error rates. For color-space alignment, CUSHAW3 is consistently one of the best aligners compared to SHRiMP2 and BFAST. The source code of CUSHAW3 and all simulated data are available at http://cushaw3.sourceforge.net.
format	article
author	Yongchao Liu Bernt Popp Bertil Schmidt
author_facet	Yongchao Liu Bernt Popp Bertil Schmidt
author_sort	Yongchao Liu
title	CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
title_short	CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
title_full	CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
title_fullStr	CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
title_full_unstemmed	CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
title_sort	cushaw3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/607ddbc33c7f428aaefb6bdec3db870f
work_keys_str_mv	AT yongchaoliu cushaw3sensitiveandaccuratebasespaceandcolorspaceshortreadalignmentwithhybridseeding AT berntpopp cushaw3sensitiveandaccuratebasespaceandcolorspaceshortreadalignmentwithhybridseeding AT bertilschmidt cushaw3sensitiveandaccuratebasespaceandcolorspaceshortreadalignmentwithhybridseeding
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CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.

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