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julien 11-22-2009 09:26 PM

Pileup to contig
I was wondering if any of you know of, or have a script to go from a pileup to series of contigs? It seems like the easiest way to get contigs from a BWA alignment but maybe someone has a better solution ?

Thank you !!!!!

lh3 11-23-2009 04:58 AM pileup2fq

colindaven 12-02-2009 05:30 AM

Also try Galaxy

They have a couple of pileup tools in the samtools section on NGS data.

Works nicely

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