Accuracy of SOLiD platform

Q:I've been getting mixed messages about the accuracy of the reads coming off the SOLiD platform. A 454 representative swore blind to me last week that only 25% of SOLiD reads are error-free (!), but this doesn't fit in with the per-base error rates I hear from other people. Can I get some insight into this from people who've been actually running these machines?

Q:The 454 rep acknowledged that their bases/run is vastly lower than their competitors (even he couldn't deny that) - but argued that their higher accuracy and longer read length made assembly so much easier that lower coverage was sufficient. On that basis he claimed that their new Titanium system (500 Mb/run) will be roughly cost-competitive with Solexa and SOLiD for at least some projects. Does that seem remotely plausible?

A:It has something to do with how the ligation primers are placed, and will give a more even (lower) error rate for all five primers. Yes, the 454 may be better for some purposes du to read length but the readlenth is likely going to increse on the Solid as well.

It's a very hard question to answer based on the uniqueness of the ligation concept, but in the simplest example, we've seen a much higher percentage of SOLiD sequences aligned to genome using any algorithm than we did with Solexa datasets.

"It's a very hard question to answer based on the uniqueness of the ligation concept, but in the simplest example, we've seen a much higher percentage of SOLiD sequences aligned to genome using any algorithm than we did with Solexa datasets."

as solid requires a colour-space aligner I find it hard to understand how 'any aligner' can be used with it to give a comparison with Solexa data which are just straight strings with Q-scores.

A:My experience of solids is that the raw read error rate is ~Q15. The two-colour changes are ~Q30. Exploiting the latter on Human requires a longer read length than is currently standard on the platform but will come soon.

The amount of alignable solexa data depends on cluster density - but at the optimum its ~95% of the PF Data (PF = non overlapping clusters). This can be ~5gigabases for a paired end run - taking 4-5days. so about 1G of alignable data (on GAII) per day provided you have optimised your cluster density for the sample.

Solid tries to align all of the data and can be very variable but typically about 20-30% align to human - im not sure of the standard solids aligner can do whole human alignments in one go - in which case you may want to look at MaQ from sanger.