Performance comparison of benchtop high-throughput sequencing platforms

[protist]

Who's Number One?
http://www.nature.com/nbt/journal/va.../nbt.2198.html

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).

[Joann]

Nicholas J. Loman

[nickloman]

Hello there!

[DICER]

can the flow space/order be utilized to reduce homopolymer errors for the Ion PGM?

[Richard Finney]

Perhaps this is a tangent (as suggested by DICER), but ... does anybody have a feel for the "homopolymer errors" in Iontorrent? How bad? How common? Can it be detected and repaired in software? Anybody have any early impressions overall about iontorrent?

[kmcarr]

Originally Posted by DICER

can the flow space/order be utilized to reduce homopolymer errors for the Ion PGM?

I noticed recently that Ion Torrent uses a more complex flow order than 454, maybe this is the reason. 454 uses the simple repeating order TACG, ad inifinitum, whereas IT's pattern is TACGTACGTCTGAGCATCGATCGATGTACAGC.

[Heisman]

Originally Posted by Richard Finney

Perhaps this is a tangent (as suggested by DICER), but ... does anybody have a feel for the "homopolymer errors" in Iontorrent? How bad? How common? Can it be detected and repaired in software? Anybody have any early impressions overall about iontorrent?

They just gave a presentation to our center and showed a plot of the rate of homopolymer mismatches over the first 5bp of a homopolymer as their algorithms keep improving, and they have improved a lot even since the softwared used in that benchtop comparison paper. However, they could have easily made the misleading as without raw data who really knows. Also, it's annoying they only showed data through the first 5 bp of a homopolymer.

I requested to them to make error profiles available as they update the software... we'll see if that happens (not getting my hopes up).