SMARTdenovo: a de novo assembler using long noisy reads

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a si...

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Autores principales:	Hailin Liu, Shigang Wu, Alun Li, Jue Ruan
Formato:	article
Lenguaje:	EN
Publicado:	GigaScience Press 2021
Materias:	Electronic computers. Computer science QA75.5-76.95
Acceso en línea:	https://doaj.org/article/3fee30aa2f144a6fb9fa8b2355ce3ab9
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id	oai:doaj.org-article:3fee30aa2f144a6fb9fa8b2355ce3ab9
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spelling	oai:doaj.org-article:3fee30aa2f144a6fb9fa8b2355ce3ab92021-12-02T17:21:21ZSMARTdenovo: a de novo assembler using long noisy reads10.46471/gigabyte.152709-4715https://doaj.org/article/3fee30aa2f144a6fb9fa8b2355ce3ab92021-03-01T00:00:00Zhttps://gigabytejournal.com/articles/15https://doaj.org/toc/2709-4715 Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a rapid assembler, which, unlike contemporaneous SMS assemblers, does not require highly accurate raw reads for error correction. It has performed well in the evaluation of congeneric assemblers and has been successfully users for various assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015; here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects. Hailin LiuShigang WuAlun LiJue RuanGigaScience PressarticleElectronic computers. Computer scienceQA75.5-76.95ENGigaByte (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Electronic computers. Computer science QA75.5-76.95
spellingShingle	Electronic computers. Computer science QA75.5-76.95 Hailin Liu Shigang Wu Alun Li Jue Ruan SMARTdenovo: a de novo assembler using long noisy reads
description	Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a rapid assembler, which, unlike contemporaneous SMS assemblers, does not require highly accurate raw reads for error correction. It has performed well in the evaluation of congeneric assemblers and has been successfully users for various assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015; here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.
format	article
author	Hailin Liu Shigang Wu Alun Li Jue Ruan
author_facet	Hailin Liu Shigang Wu Alun Li Jue Ruan
author_sort	Hailin Liu
title	SMARTdenovo: a de novo assembler using long noisy reads
title_short	SMARTdenovo: a de novo assembler using long noisy reads
title_full	SMARTdenovo: a de novo assembler using long noisy reads
title_fullStr	SMARTdenovo: a de novo assembler using long noisy reads
title_full_unstemmed	SMARTdenovo: a de novo assembler using long noisy reads
title_sort	smartdenovo: a de novo assembler using long noisy reads
publisher	GigaScience Press
publishDate	2021
url	https://doaj.org/article/3fee30aa2f144a6fb9fa8b2355ce3ab9
work_keys_str_mv	AT hailinliu smartdenovoadenovoassemblerusinglongnoisyreads AT shigangwu smartdenovoadenovoassemblerusinglongnoisyreads AT alunli smartdenovoadenovoassemblerusinglongnoisyreads AT jueruan smartdenovoadenovoassemblerusinglongnoisyreads
_version_	1718381021292920832

SMARTdenovo: a de novo assembler using long noisy reads

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