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Old 05-16-2010, 11:28 PM   #1
francesco.vezzi
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Default mixing long and short sequences

Hi all
I'm trying to assembly a plant genome using a 70X coverage formed by Illumina reads (75 bases). Some days ago it turned out that we have also a set of Sanger paired reads belonging to the same genome, so I was wondering how to integrate this extra information in the assembly process.

One "simple" way is to perform de novo assembly using only short Illumina reads and then use Sanger reads to validate and perform scaffolding. But another possibility is to give the long reads directly to SOAPdenovo or ABySS.

As far as I know de bruijn graph assemblers don't work well with long reads like the sanger ones, but I was wondering if someone has already tried this approach and it he/she succeed.....

It will also be interesting know if somebody has used some hybrid approach or some tools designed to handle this kind of problem

Thanks
Francesco
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Old 05-19-2010, 09:10 AM   #2
spenthil
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Take a look at Velvet, the Rock Band algorithm uses long reads to resolve ambiguities in the de Bruijn graph.
http://www.plosone.org/article/info:...E6496DEB07A63C
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