A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befit...

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Autores principales:	Wenyu Zhang, Jiajia Chen, Yang Yang, Yifei Tang, Jing Shang, Bairong Shen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/69029e9f7f26429ebab84eaf356a5370
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id	oai:doaj.org-article:69029e9f7f26429ebab84eaf356a5370
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spelling	oai:doaj.org-article:69029e9f7f26429ebab84eaf356a53702021-11-18T06:57:20ZA practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.1932-620310.1371/journal.pone.0017915https://doaj.org/article/69029e9f7f26429ebab84eaf356a53702011-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21423806/?tool=EBIhttps://doaj.org/toc/1932-6203The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM) occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers.Wenyu ZhangJiajia ChenYang YangYifei TangJing ShangBairong ShenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 3, p e17915 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wenyu Zhang Jiajia Chen Yang Yang Yifei Tang Jing Shang Bairong Shen A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
description	The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM) occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers.
format	article
author	Wenyu Zhang Jiajia Chen Yang Yang Yifei Tang Jing Shang Bairong Shen
author_facet	Wenyu Zhang Jiajia Chen Yang Yang Yifei Tang Jing Shang Bairong Shen
author_sort	Wenyu Zhang
title	A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
title_short	A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
title_full	A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
title_fullStr	A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
title_full_unstemmed	A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
title_sort	practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/69029e9f7f26429ebab84eaf356a5370
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A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

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