Commercially available benchtop sequencers differ in accuracy, throughput, and read length.

  • Major finding: Commercially available benchtop sequencers differ in accuracy, throughput, and read length.

  • Approach: The same E. coli isolate was sequenced with 3 different benchtop high-throughput sequencers.

  • Impact: An unbiased performance, time, and cost comparison can inform laboratory purchasing decisions.

DNA sequencing technology has advanced and equipment costs have decreased to the point where benchtop instruments are now available and affordable for many clinical and research laboratories. Loman and colleagues report the results of a performance comparison between 3 commercially available benchtop high-throughput sequencing instruments: the Roche 454 GS Junior, the Illumina MiSeq, and the Life Technologies Ion Torrent Personal Genome Machine (PGM). The authors used each instrument to sequence an Escherichia coli isolate and calculated a quality score for each sequencer by aligning reads to a reference genome and identifying nucleotide substitutions, insertions, and deletions independently of the manufacturer's analysis software. Notably, there was a high degree of variation in the number, length, accuracy, and genome coverage of reads produced by the 3 sequencers. The MiSeq, the only instrument that does not require manual preparation of amplified sequence libraries, produced a much higher number of reads and had significantly fewer errors than the 454 GS Junior or the Ion Torrent PGM. However, the MiSeq is the most expensive of the instruments and had the longest run time. The least expensive instrument, the Ion Torrent PGM, also had the shortest read time, but produced short reads with the most errors and gaps and covered the least of the reference genome. The 454 GS Junior obtained the longest reads, but had a much lower total number of reads than the other machines, resulting in the highest cost per megabase sequenced. This unbiased analysis, which reveals advantages and disadvantages of each sequencer, may be informative to those considering benchtop high-throughput sequencing instruments for their laboratories.

Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012;30:434–9.

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