Table 2.
Platform | Manufacturer | Throughput (per machine run) | Reported errors | Depth (virus) | Depth (bacteria) | Reference |
---|---|---|---|---|---|---|
454 GS Junior |
Roche |
~135 K reads @ ~520 nt |
~0.38% indels |
7 K |
14 |
[26] |
GS-FLX Titanium |
Roche |
~1 M reads @ ~500 nt |
~0.28% indels; ~0.12% substitution (max 1.07%) |
50 K |
100 |
[27] |
MiSeq |
Illumina |
~ 11 M reads @ ~ 150 nt |
< 0.001% indels, ~0.1% substitutions |
165 K |
330 |
[26] |
GA IIx |
Illumina |
~ 640 M reads @ 100 nt |
~0.001% indels; ~0.31% substitutions (max ~5.85%) |
6 M |
13 K |
[27] |
HiSeq 2000 |
Illumina |
~ 6G reads @ 100 nt |
~0.002% indels; ~0.32% substitutions (max ~8.2%) |
60 M |
120 K |
* |
Ion Torrent PGM |
Life technologies |
~2 M reads @ ~121 nt |
~1.5% indels |
24 K |
48 |
[26] |
SOLiD |
Life technologies |
~120 M reads @ ~50 nt |
~0.09% substitutions (max > 5%) |
600 K |
1 K |
[28,29] |
RS |
Pacific biosystems |
~200 K reads @ ~2000 nt (max > 15000 nt) |
~14% indels, ~1% substitutions |
40 K |
80 |
[30,31] |
tSMS | Helicos | ~1G reads @ 35 nt | ~3% indels, ~0.2% substitutions | 3 M | 7 K | [32] |
Indels errors are largely associated with homopolymers for Roche and Ion Torrent. This fact can have a significant impact on the detection of variants associated with homopolymers, as was recently shown for the 2184delA mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) using Ion Torrent PGM [33]. Sequencing errors are also highly dependent on the sequencing context and thus can influence variant calling in a biased, but potentially predictable way. For example, certain GC-rich motifs have been reported to have substitution errors of close to 6% [27] for the Illumina sequencing technology. Depth columns give anticipated read depth for a typical viral (~10 K) or bacterial (~5 M) genome.
*Calculated for this review from control PhiX data using GemSIM v1.6 [27].