Table 1.
Summary of Roche 454, Illumina GA and ABI SOLiD seqeuncing capabilities.
| Roche 454 FLX Titanium | Illumina Solexa GA | ABI SOLiD 3 | |
|---|---|---|---|
| Reads per run (M) | 1.25 | 250 | 320 |
| Average read length (bp)a | 330 | 75 or 100 | 50 |
| Usable reads that pass quality filtersb | > 99.5% | 55% | 35% |
| Raw accuracy readsc | 96.0–97.0% | 96.2–99.7% | 99.0 to > 99.9%d |
| Primary bias | Homopolymer read errors | short read length | short read length |
| Biases in eukaryotic sequencingb | Minimal low coverage of AT‐rich regions | Low coverage in AT‐rich repetitive regions | Low coverage in AT‐rich repetitive regions |
| Amplicon overrepresentation in 50 bp end regionsb | 5% | 56% | 11% (after amplicon end removal) |
| Saturating level of redundant sequence coverageb | 43× | 188× | 841× |
a.
Reviewed by Metzker (2010).
b.
Reviewed by Harismendy and colleagues (2009).
c.
Reviewed by Chan (2009).
d.
Higher accuracy achieved by reading each base twice in a two‐base encoding scheme.