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Performance comparison of benchtop high-throughput sequencing platforms
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Loman, Nicholas J., Misra, Raju V., Dallman, Timothy J., Constantinidou, Chrystala, Gharbia, Saheer E., Wain, John and Pallen, Mark J. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, Volume 30 (Number 5). pp. 434-439. doi:10.1038/nbt.2198 ISSN 1087-0156.
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Official URL: http://dx.doi.org/10.1038/nbt.2198
Abstract
Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. The MiSeq had the highest throughput per run (1.6 Gb/run, 60 Mb/h) and lowest error rates. The 454 GS Junior generated the longest reads (up to 600 bases) and most contiguous assemblies but had the lowest throughput (70 Mb/run, 9 Mb/h). Run in 100-bp mode, the Ion Torrent PGM had the highest throughput (80–100 Mb/h). Unlike the MiSeq, the Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors (1.5 and 0.38 errors per 100 bases, respectively).
Item Type: | Journal Article | ||||
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Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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Journal or Publication Title: | Nature Biotechnology | ||||
Publisher: | Nature Publishing Group | ||||
ISSN: | 1087-0156 | ||||
Official Date: | May 2012 | ||||
Dates: |
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Volume: | Volume 30 | ||||
Number: | Number 5 | ||||
Page Range: | pp. 434-439 | ||||
DOI: | 10.1038/nbt.2198 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Description: | Nat. Biotechnol. 30, 434–439 (2012); published online 22 April 2012; corrected online 23 April 2012; corrected after print 7 June 2012 In the version of this article initially published online, in the Online Methods “Ion Torrent Sequencing” section, the sentence beginning with “Ten milligrams of this DNA was fragmented with a Bioruptor instrument....” should have read “Ten micrograms....” and in the “454 GS Junior sequencing” section, “(500 total)” should have read “(500 ng total).” The errors have been corrected in the PDF and HTML versions of this article. |
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