Evaluating coverage bias in next-generation sequencing of Escherichia coli.

Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed th...

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Autores principales:	Samantha Gunasekera, Sam Abraham, Marc Stegger, Stanley Pang, Penghao Wang, Shafi Sahibzada, Mark O'Dea
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/604c8887697b49bcaa926d0901615952
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spelling	oai:doaj.org-article:604c8887697b49bcaa926d09016159522021-12-02T20:10:09ZEvaluating coverage bias in next-generation sequencing of Escherichia coli.1932-620310.1371/journal.pone.0253440https://doaj.org/article/604c8887697b49bcaa926d09016159522021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253440https://doaj.org/toc/1932-6203Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.Samantha GunasekeraSam AbrahamMarc SteggerStanley PangPenghao WangShafi SahibzadaMark O'DeaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 6, p e0253440 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Samantha Gunasekera Sam Abraham Marc Stegger Stanley Pang Penghao Wang Shafi Sahibzada Mark O'Dea Evaluating coverage bias in next-generation sequencing of Escherichia coli.
description	Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.
format	article
author	Samantha Gunasekera Sam Abraham Marc Stegger Stanley Pang Penghao Wang Shafi Sahibzada Mark O'Dea
author_facet	Samantha Gunasekera Sam Abraham Marc Stegger Stanley Pang Penghao Wang Shafi Sahibzada Mark O'Dea
author_sort	Samantha Gunasekera
title	Evaluating coverage bias in next-generation sequencing of Escherichia coli.
title_short	Evaluating coverage bias in next-generation sequencing of Escherichia coli.
title_full	Evaluating coverage bias in next-generation sequencing of Escherichia coli.
title_fullStr	Evaluating coverage bias in next-generation sequencing of Escherichia coli.
title_full_unstemmed	Evaluating coverage bias in next-generation sequencing of Escherichia coli.
title_sort	evaluating coverage bias in next-generation sequencing of escherichia coli.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/604c8887697b49bcaa926d0901615952
work_keys_str_mv	AT samanthagunasekera evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli AT samabraham evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli AT marcstegger evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli AT stanleypang evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli AT penghaowang evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli AT shafisahibzada evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli AT markodea evaluatingcoveragebiasinnextgenerationsequencingofescherichiacoli
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Evaluating coverage bias in next-generation sequencing of Escherichia coli.

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