Read length versus depth of coverage for viral quasispecies reconstruction.

Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different un...

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Autores principales:	Osvaldo Zagordi, Martin Däumer, Christian Beisel, Niko Beerenwinkel
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/42bf5731f7b64b8e9514c07959769ef2
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spelling	oai:doaj.org-article:42bf5731f7b64b8e9514c07959769ef22021-11-18T08:13:16ZRead length versus depth of coverage for viral quasispecies reconstruction.1932-620310.1371/journal.pone.0047046https://doaj.org/article/42bf5731f7b64b8e9514c07959769ef22012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23056573/?tool=EBIhttps://doaj.org/toc/1932-6203Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.Osvaldo ZagordiMartin DäumerChristian BeiselNiko BeerenwinkelPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e47046 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Osvaldo Zagordi Martin Däumer Christian Beisel Niko Beerenwinkel Read length versus depth of coverage for viral quasispecies reconstruction.
description	Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.
format	article
author	Osvaldo Zagordi Martin Däumer Christian Beisel Niko Beerenwinkel
author_facet	Osvaldo Zagordi Martin Däumer Christian Beisel Niko Beerenwinkel
author_sort	Osvaldo Zagordi
title	Read length versus depth of coverage for viral quasispecies reconstruction.
title_short	Read length versus depth of coverage for viral quasispecies reconstruction.
title_full	Read length versus depth of coverage for viral quasispecies reconstruction.
title_fullStr	Read length versus depth of coverage for viral quasispecies reconstruction.
title_full_unstemmed	Read length versus depth of coverage for viral quasispecies reconstruction.
title_sort	read length versus depth of coverage for viral quasispecies reconstruction.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/42bf5731f7b64b8e9514c07959769ef2
work_keys_str_mv	AT osvaldozagordi readlengthversusdepthofcoverageforviralquasispeciesreconstruction AT martindaumer readlengthversusdepthofcoverageforviralquasispeciesreconstruction AT christianbeisel readlengthversusdepthofcoverageforviralquasispeciesreconstruction AT nikobeerenwinkel readlengthversusdepthofcoverageforviralquasispeciesreconstruction
_version_	1718422038489595904

Read length versus depth of coverage for viral quasispecies reconstruction.

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