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Performance comparison of benchtop high-throughput sequencing platforms
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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).