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Performance comparison of benchtop high-throughput sequencing platforms

Loman, N. J. and Misra, Raju V and Dallman, Timothy J and Constantinidou, Chrystala and Gharbia, Saheer E and Wain, John and Pallen, Mark J. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30 (5). pp. 434-439. ISSN 1087-0156

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URL of Published Version: http://dx.doi.org/10.1038/nbt.2198

Identification Number/DOI: doi:10.1038/nbt.2198

Three bench-top 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 a draft bacterial genome sequence in days, making them attractive for use in the identification and characterization of pathogens in the clinical setting. We compared the performance of these instruments by sequencing isolates of Escherichia coli O104:H4 from the German outbreak of 2011. We compared performance of the platforms, analysing throughput, read length, read error profile and rate, de novo assembly quality and completeness. MiSeq had the highest throughput and lowest error rate. The 454 Junior generated the longest reads and best assemblies. The Ion Torrent PGM produced intermediate throughput with the shortest reads. The Ion Torrent PGM and 454 GS Junior both suffer from errors in homopolymers.

Type of Work:Article
Date:April 2012 (Publication)
School/Faculty:Colleges (2008 onwards) > College of Life & Environmental Sciences
Department:School of Biosciences
Subjects:QH426 Genetics
QR180 Immunology
RA Public aspects of medicine
Institution:University of Birmingham
Copyright Holders:Nature America, Inc, the authors
ID Code:1166
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