A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
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DOI：
10.1186/1471-2164-13-341
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发表时间：
2012-07-24
期刊：
影响因子：
4.4
通讯作者：
Gu Y
中科院分区：
文献类型：
--
作者：
Quail MA;Smith M;Coupland P;Otto TD;Harris SR;Connor TR;Bertoni A;Swerdlow HP;Gu Y
下一代测序（NGS）技术已经彻底改变了基因组和遗传研究。这一领域的变化速度很快，2011年发布了三个主要的新测序平台：Ion Torrent的PGM、Pacific Biosciences的RS和Illumina MiSeq。在这里，我们将这些平台获得的结果与当前市场领导者Illumina HiSeq的性能进行了比较。为了比较这些平台，并获得足够的覆盖深度以进行有意义的分析，我们对一组4种微生物基因组进行了测序，平均GC含量范围为19.3%至67.7%。总之，这些代表了基因组内容的全面范围。在这里，我们报告了我们对序列数据的覆盖率分布，偏倚，GC分布，变异检测和准确性的分析。由Ion Torrent、MiSeq和Pacific Biosciences技术生成的序列在富含GC、中性和适度富含AT的基因组上显示出近乎完美的覆盖行为，但在对PGM上的恶性疟原虫极其富含AT的基因组进行测序时观察到了深刻的偏差，导致约30%的基因组没有覆盖。我们分析了从每个平台调用变体的能力，发现与MiSeq数据相比，我们可以从Ion Torrent数据调用更多的变体，但代价是更高的假阳性率。来自Pacific Biosciences数据的变异呼叫是可能的，但需要更高的覆盖深度。在PGM和MiSeq数据中均观察到背景特异性错误，但在Pacific Biosciences平台中未观察到。这里评估的所有三个快速周转测序仪都能够生成可用的序列。然而，这些数据的质量和它将支持的应用程序之间存在关键差异。
Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.
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影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
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通讯作者：
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影响因子：
64.8
作者：
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通讯作者：
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