lra: A long read aligner for sequences and contigs.

It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact matches are found between the sequence and the geno...

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Autores principales:	Jingwen Ren, Mark J P Chaisson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/374191bdee9242da9ac6ee49931ee816
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spelling	oai:doaj.org-article:374191bdee9242da9ac6ee49931ee8162021-11-25T05:40:36Zlra: A long read aligner for sequences and contigs.1553-734X1553-735810.1371/journal.pcbi.1009078https://doaj.org/article/374191bdee9242da9ac6ee49931ee8162021-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009078https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact matches are found between the sequence and the genome. While straightforward implementations of SDP penalize gaps with a cost that is a linear function of gap length, biological variation is more accurately represented when gap cost is a concave function of gap length. We have developed a method, lra, that uses SDP with a concave-cost gap penalty, and used lra to align long-read sequences from PacBio and Oxford Nanopore (ONT) instruments as well as de novo assembly contigs. This alignment approach increases sensitivity and specificity for SV discovery, particularly for variants above 1kb and when discovering variation from ONT reads, while having runtime that are comparable (1.05-3.76×) to current methods. When applied to calling variation from de novo assembly contigs, there is a 3.2% increase in Truvari F1 score compared to minimap2+htsbox. lra is available in bioconda (https://anaconda.org/bioconda/lra) and github (https://github.com/ChaissonLab/LRA).Jingwen RenMark J P ChaissonPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 6, p e1009078 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jingwen Ren Mark J P Chaisson lra: A long read aligner for sequences and contigs.
description	It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact matches are found between the sequence and the genome. While straightforward implementations of SDP penalize gaps with a cost that is a linear function of gap length, biological variation is more accurately represented when gap cost is a concave function of gap length. We have developed a method, lra, that uses SDP with a concave-cost gap penalty, and used lra to align long-read sequences from PacBio and Oxford Nanopore (ONT) instruments as well as de novo assembly contigs. This alignment approach increases sensitivity and specificity for SV discovery, particularly for variants above 1kb and when discovering variation from ONT reads, while having runtime that are comparable (1.05-3.76×) to current methods. When applied to calling variation from de novo assembly contigs, there is a 3.2% increase in Truvari F1 score compared to minimap2+htsbox. lra is available in bioconda (https://anaconda.org/bioconda/lra) and github (https://github.com/ChaissonLab/LRA).
format	article
author	Jingwen Ren Mark J P Chaisson
author_facet	Jingwen Ren Mark J P Chaisson
author_sort	Jingwen Ren
title	lra: A long read aligner for sequences and contigs.
title_short	lra: A long read aligner for sequences and contigs.
title_full	lra: A long read aligner for sequences and contigs.
title_fullStr	lra: A long read aligner for sequences and contigs.
title_full_unstemmed	lra: A long read aligner for sequences and contigs.
title_sort	lra: a long read aligner for sequences and contigs.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/374191bdee9242da9ac6ee49931ee816
work_keys_str_mv	AT jingwenren lraalongreadalignerforsequencesandcontigs AT markjpchaisson lraalongreadalignerforsequencesandcontigs
_version_	1718414511509078016

lra: A long read aligner for sequences and contigs.

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