title: Performance comparison of benchtop high-throughput sequencing platforms.
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).
authors.affiliation: Centre for Systems Biology, University of Birmingham, Birmingham, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.forename: Raju V
authors.initials: RV
authors.lastname: Misra
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Dallman
authors.forename: Chrystala
authors.initials: C
authors.lastname: Constantinidou
authors.forename: Saheer E
authors.initials: SE
authors.lastname: Gharbia
authors.forename: John
authors.initials: J
authors.lastname: Wain
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020451:Contig Mapping; D004867:Equipment Design; D004926:Escherichia coli / Q000235:genetics; D004927:Escherichia coli Infections / Q000382:microbiology; D015723:Gene Library; D016680:Genome, Bacterial; D006801:Humans; D016133:Polymerase Chain Reaction / Q000191:economics / Q000295:instrumentation; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000191:economics / Q000295:instrumentation* / Q000379:methods*