An integrated pipeline for de novo assembly of microbial genomes.

Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi...

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Autores principales:	Andrew Tritt, Jonathan A Eisen, Marc T Facciotti, Aaron E Darling
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d171c67994c14df3adb5755987004490
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spelling	oai:doaj.org-article:d171c67994c14df3adb57559870044902021-11-18T07:05:45ZAn integrated pipeline for de novo assembly of microbial genomes.1932-620310.1371/journal.pone.0042304https://doaj.org/article/d171c67994c14df3adb57559870044902012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23028432/?tool=EBIhttps://doaj.org/toc/1932-6203Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron's Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the other assembly algorithm. In particular, the assemblies produced by A5 exhibit 50% or more reduction in broken protein coding sequences relative to SOAPdenovo assemblies. The A5 pipeline can also assemble Illumina sequence data from libraries constructed by the Nextera (transposon-catalyzed) protocol, which have markedly different characteristics to mechanically sheared libraries. Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage.Andrew TrittJonathan A EisenMarc T FacciottiAaron E DarlingPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e42304 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Andrew Tritt Jonathan A Eisen Marc T Facciotti Aaron E Darling An integrated pipeline for de novo assembly of microbial genomes.
description	Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron's Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the other assembly algorithm. In particular, the assemblies produced by A5 exhibit 50% or more reduction in broken protein coding sequences relative to SOAPdenovo assemblies. The A5 pipeline can also assemble Illumina sequence data from libraries constructed by the Nextera (transposon-catalyzed) protocol, which have markedly different characteristics to mechanically sheared libraries. Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage.
format	article
author	Andrew Tritt Jonathan A Eisen Marc T Facciotti Aaron E Darling
author_facet	Andrew Tritt Jonathan A Eisen Marc T Facciotti Aaron E Darling
author_sort	Andrew Tritt
title	An integrated pipeline for de novo assembly of microbial genomes.
title_short	An integrated pipeline for de novo assembly of microbial genomes.
title_full	An integrated pipeline for de novo assembly of microbial genomes.
title_fullStr	An integrated pipeline for de novo assembly of microbial genomes.
title_full_unstemmed	An integrated pipeline for de novo assembly of microbial genomes.
title_sort	integrated pipeline for de novo assembly of microbial genomes.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/d171c67994c14df3adb5755987004490
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An integrated pipeline for de novo assembly of microbial genomes.

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