>What would you do with 10kbp reads?

>I just caught a tweet about an article on the Pathogens blog (What can you do with 1000 base pair reads?), which is specifically about 454 reads. Personally, I’m not so interested in 454 reads – the technology is good, but I don’t have access to 454 data, so it’s somewhat irrelevant to me. (Not to say 1kbp reads isn’t neat, but no one has volunteered to pass me 454 data in a long time…)

So, anyhow, I’m trying to think two steps ahead. 2010 is supposed to be the year that Pacific Biosciences (and other companies) release the next generation of sequencing technologies – which will undoubtedly be longer than 1k. (I seem to recall hearing that PacBio has 10k+ reads.- UPDATE: I found a reference.) So to heck with 1kbp reads, this raises the real question: What would you do with a 10,000bp read? And, equally important, how do you work with a 10kbp read?

  • What software do you have now that can deal with 10k reads?
  • Will you align or assemble with a 10k read?
  • What experiments will you be able to do with a 10k read?

Frankly, I suspect that nothing we’re currently using will work well with them – we’ll all have to go back to the drawing board and rework the algorithms we use.

So, what do you think?

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