Performance comparison of benchtop high-throughput sequencing platforms
Performance comparison of benchtop high-throughput sequencing platforms
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DOI：
10.1038/nbt.2198
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发表时间：
2012-05-01
影响因子：
46.9
通讯作者：
Pallen, Mark J.
中科院分区：
文献类型：
--
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
现在有三种台式高通量测序仪器可供使用。454 GS Junior（Roche）、MiSeq（Illumina）和Ion Torrent PGM（Life Technologies）都是激光打印机大小，设置和运行成本适中。每台仪器都可以在几天内生成细菌基因组序列草案所需的数据，这使得它们在临床环境中识别和表征病原体方面具有吸引力。我们通过对2011年在德国引起食物中毒的大肠杆菌O 104：H4分离株进行测序，比较了这些仪器的性能。MiSeq具有最高的每次运行吞吐量（1.6 Gb/run，60 Mb/h）和最低的错误率。454 GS Junior产生最长的读取（高达600个碱基）和最连续的组装，但具有最低的通量（70 Mb/运行，9 Mb/h）。在100 bp模式下运行，Ion Torrent PGM具有最高的通量（80-100 Mb/h）。与MiSeq不同，Ion Torrent PGM和454 GS Junior都产生了均聚物相关的indel错误（每100个碱基分别有1.5和0.38个错误）。
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).