How to generate de novo assembly sequence from complete genomics data?

[ssnowfox]

Hi, all,
recently we got a few samples' sequence data from complete genomics, we hope to generate a de novo assembly sequence. But i didn't find any tool would support complete genomics platform, some tools like Velvet, SOAPdenovo, ABySS, could be used for de novo assembly for data generated from Solexa or Illumina. And the complete genomics data format is somewhat different from that of other platforms. Does anybody has some good suggestion?

Thanks

[agrewal]

Hi ssnowfox,

To the best of our knowledge, currently available de novo methods are not appropriate for our read structure. Devising a de novo assembly method that takes into account specific characteristics of our read structure is an active development area for us, and we hope to utilize such approaches in future versions of our pipeline.

You may want to contact [email protected] to see if there are other ways to find the answer to the problem you are trying to address with de novo assembly. It’s possible, for instance, that the newest release of our assembly pipeline, v2.0 (which can be applied to older samples through our re-analysis service) could be potentially useful for your purposes.

Regards,
Anoop Grewal

Director, Customer Support
Complete Genomics

[Pseudonym]

I took a quick look around the web site and couldn't find any information on the formats, or any explanation of why current de novo assemblers couldn't be adapted for them. Is it just a syntax problem, or is there some technical reason?