Abstract
With fast development and wide applications of next generation sequencing (NGS), genomic sequence information is within reach to various research fields. Three benchtop NGS instruments are now available. The 454 GS Junior (Roche), Ion PGM (Life Technologies) and MiSeq (Illumina) are laser-printer sized and offer modest set-up and running costs. By reviewing 2 studies that compared the performance of these instruments, the major characteristics of each benchtop platforms are compared to enable direct comparisons. The 454 GS Junior generated the longest reads and most contiguous assemblies but had the lowest throughput. The Ion Torrent PGM had the highest throughput and fastest run time. The MiSeq had the highest throughput per run and lowest error rates. The Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors. Although all the platforms allow multiplexing of samples, details of experimental design, library preparation and data analysis may constrain the options. The features of the platforms provide opportunities both to conduct groundbreaking studies and to waste money. Thus, careful considerations should be made before purchasing or using any of them.
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Table 1.
Comparison of benchtop instruments and sequencing runs (modified from reference # 2)
Table 2.
Run and alignment metrics for benchtop sequencers (modified from reference # 2)
Metrics for each sequencing run are shown as well as results of alignment against the reference sequence. Depth of coverage for the chromosome and two large plasmids (pESBL and pAA) are shown with the percentage of read that align. For the MiSeq run, the sequence metrics are shown for the entire run as well as the results of de-multiplexing E. coli O104:H4 strain 280.
Table 3.
Insertion/deletion and substitution errors on read level for benchtop sequencer (modified from reference # 3)
Table 4.
Comparison between Ion PGM and MiSeq sequencing performance in 10 positive controls (modified from reference # 4)
Ion PGM (TMAP*) | MiSeq | |
---|---|---|
Total read (Mb) | 295.97 | 469.42 |
Average read length (bp) | 116 | 150 |
% mapped on human genome | 96.8% | 75% |
% on target regions | 26.7% | 22.7% |
Mean depth of coverage | 63 | 95 |
% of target regions at > 10-fold coverage | 93.7% | 96.8% |
% of target regions at > 20-fold coverage | 85.9% | 93.2% |