Comparison of sequence reads obtained from three next-generation sequencing platforms.

Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequen...

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Autores principales:	Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/15678aee2ddd4bed95e911b6e82ec463
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id	oai:doaj.org-article:15678aee2ddd4bed95e911b6e82ec463
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spelling	oai:doaj.org-article:15678aee2ddd4bed95e911b6e82ec4632021-11-18T06:53:51ZComparison of sequence reads obtained from three next-generation sequencing platforms.1932-620310.1371/journal.pone.0019534https://doaj.org/article/15678aee2ddd4bed95e911b6e82ec4632011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21611185/?tool=EBIhttps://doaj.org/toc/1932-6203Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX), Illumina Genome Analyzer (GA), and Applied Biosystems SOLiD system (SOLiD). A common genomic DNA sample obtained from Escherichia coli strain DH1 was applied to these sequencers. The obtained sequence reads were aligned to the complete genome sequence of E. coli DH1, to evaluate the accuracy and sequence bias of these sequence methods. We found that the fraction of "junk" data, which could not be aligned to the reference genome, was largest in the data set of SOLiD, in which about half of reads could not be aligned. Among data sets after alignment to the reference, sequence accuracy was poorest in GA data sets, suggesting relatively low fidelity of the elongation reaction in the GA method. Furthermore, by aligning the sequence reads to the E. coli strain W3110, we screened sequence differences between two E. coli strains using data sets of three different next-generation platforms. The results revealed that the detected sequence differences were similar among these three methods, while the sequence coverage required for the detection was significantly small in the FLX data set. These results provided valuable information on the quality of short sequence reads and the performance of SNP detection in three next-generation sequencing platforms.Shingo SuzukiNaoaki OnoChikara FurusawaBei-Wen YingTetsuya YomoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 5, p e19534 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shingo Suzuki Naoaki Ono Chikara Furusawa Bei-Wen Ying Tetsuya Yomo Comparison of sequence reads obtained from three next-generation sequencing platforms.
description	Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX), Illumina Genome Analyzer (GA), and Applied Biosystems SOLiD system (SOLiD). A common genomic DNA sample obtained from Escherichia coli strain DH1 was applied to these sequencers. The obtained sequence reads were aligned to the complete genome sequence of E. coli DH1, to evaluate the accuracy and sequence bias of these sequence methods. We found that the fraction of "junk" data, which could not be aligned to the reference genome, was largest in the data set of SOLiD, in which about half of reads could not be aligned. Among data sets after alignment to the reference, sequence accuracy was poorest in GA data sets, suggesting relatively low fidelity of the elongation reaction in the GA method. Furthermore, by aligning the sequence reads to the E. coli strain W3110, we screened sequence differences between two E. coli strains using data sets of three different next-generation platforms. The results revealed that the detected sequence differences were similar among these three methods, while the sequence coverage required for the detection was significantly small in the FLX data set. These results provided valuable information on the quality of short sequence reads and the performance of SNP detection in three next-generation sequencing platforms.
format	article
author	Shingo Suzuki Naoaki Ono Chikara Furusawa Bei-Wen Ying Tetsuya Yomo
author_facet	Shingo Suzuki Naoaki Ono Chikara Furusawa Bei-Wen Ying Tetsuya Yomo
author_sort	Shingo Suzuki
title	Comparison of sequence reads obtained from three next-generation sequencing platforms.
title_short	Comparison of sequence reads obtained from three next-generation sequencing platforms.
title_full	Comparison of sequence reads obtained from three next-generation sequencing platforms.
title_fullStr	Comparison of sequence reads obtained from three next-generation sequencing platforms.
title_full_unstemmed	Comparison of sequence reads obtained from three next-generation sequencing platforms.
title_sort	comparison of sequence reads obtained from three next-generation sequencing platforms.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/15678aee2ddd4bed95e911b6e82ec463
work_keys_str_mv	AT shingosuzuki comparisonofsequencereadsobtainedfromthreenextgenerationsequencingplatforms AT naoakiono comparisonofsequencereadsobtainedfromthreenextgenerationsequencingplatforms AT chikarafurusawa comparisonofsequencereadsobtainedfromthreenextgenerationsequencingplatforms AT beiwenying comparisonofsequencereadsobtainedfromthreenextgenerationsequencingplatforms AT tetsuyayomo comparisonofsequencereadsobtainedfromthreenextgenerationsequencingplatforms
_version_	1718424213094662144

Comparison of sequence reads obtained from three next-generation sequencing platforms.

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