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Performance comparison of benchtop high-throughput sequencing platforms

A Corrigendum to this article was published on 07 June 2012

This article has been updated

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).

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Figure 1: Evaluation of read length and quality from benchtop sequencers.
Figure 2: N50 contig sizes from assemblies generated from sequence data for each sequencing platform.
Figure 3: An analysis of gaps when aligning draft de novo assemblies to the reference genome.

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Sequence Read Archive

Change history

  • 23 April 2012

    On page 2, “error rates” has been corrected to “quality scores” in the sentence “Alignment quality scores measured in this way generally had good agreement with predicted scores, with the Ion Torrent PGM generally underestimating error rates and the other instruments slightly overestimating them (Supplementary Fig. 2).” The corrected sentence reads “Alignment quality scores measured in this way generally had good agreement with predicted scores, with the Ion Torrent PGM generally underestimating quality scores and the other instruments slightly overestimating them (Supplementary Fig. 2).”

  • 07 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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Acknowledgements

We gratefully acknowledge the blogging community for helpful discussion in the comments section of our blog (http://pathogenomics.bham.ac.uk/blog/), and in particular to B. Chevreux, J. Johnson, K. Robison and L. Nederbragt. We are grateful to C. Hercus at Novocraft for help with the Novoalign software and to A. Darling for help with Mauve Assembly Metrics. We thank Roche Diagnostics, UK, for 454 GS FLX+ and 454 FLX paired-end sequencing, technical support and helpful discussion. We thank Life Technologies for early access to 316 chips and instrument fluidics upgrade. We thank G. Smith and Illumina UK for early access to the MiSeq platform and public release of E. coli outbreak-strain data. We thank the three anonymous reviewers for their many helpful suggestions for improving the manuscript. The xBASE facility and N.J.L. are funded by BBSRC grant BBE0111791.

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Authors and Affiliations

Authors

Contributions

N.J.L., J.W., S.E.G. and M.J.P. conceived the experiments; J.W. and S.G. supplied the strains; N.J.L., R.V.M. and T.J.D. carried out the bioinformatics analysis; C.C. performed the Ion Torrent sequencing; and S.E.G. and R.V.M. performed the 454 GS Junior sequencing. N.J.L. and M.J.P. wrote the manuscript. All authors commented on the manuscript.

Corresponding authors

Correspondence to John Wain or Mark J Pallen.

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Competing interests

Mark J. Pallen was a winner of an Ion Torrent Personal Genome Machine in the European PGM grant program. Nicholas J. Loman has had expenses paid to speak at an Ion Torrent meeting organized by Life Technologies, and has received honoraria and expenses to speak at Illumina meetings. The other authors declare no financial interest.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1-3 and Supplementary Figs. 1-5 (PDF 1037 kb)

Supplementary Table 4

Statistics from Mauve Assembly Metrics comparing each of the assemblies produced from bench-top instrument data (XLSX 13 kb)

Supplementary Table 5

Result of BLAST searches for important pathogen biology genes (XLSX 39 kb)

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Loman, N., Misra, R., Dallman, T. et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30, 434–439 (2012). https://doi.org/10.1038/nbt.2198

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