小型测序仪一般只有台式电脑大小，价格便宜、操作简单，但通量相对较小，一般用于重测序和小基因组或基因组片段的de novo测序
Nicholas Loman在Nature Biotechnology发了一篇文章，综合比较了三个小型测序仪，454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies)，并且接受了Nature的采访。
这三个测序仪都有各自的优缺点。PGM单位时间内通量高；MiSeq每个run通量高；MiSeq错误率低，454可读取最长的序列片段但通量低；PGM和454在测重复序列时容易出错，且多次重复测序仍然无法消除；MiSeq整体稳定性和质量较好。价格方面没有透露。我所了解到的是MiSeq比PGM高一点，454最贵，但PGM更新换代花费少，只需要更新一个芯片。
有兴趣的可以读读这篇文章：
Performance comparison of benchtop high-throughput sequencing platforms
Nicholas J Loman, Raju V Misra, Timothy J Dallman, Chrystala Constantinidou, Saheer E Gharbia, John Wain & Mark J Pallen
Nature Biotechnology 30, 434–439 (2012) doi:10.1038/nbt.2198
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 coliO104: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).
全文链接：http://www.nature.com/nbt/journal/v30/n5/full/nbt.2198.html
采访的全文记录：http://www.nature.com/news/next-generation-genome-sequencers-compared-1.10497
参考：http://bioops.info/2012/04/desktop-sequencers-comparison/
