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Old 11-22-2009, 09:26 PM   #1
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Default 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 !!!!!
julien is offline   Reply With Quote
Old 11-23-2009, 04:58 AM   #2
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Default pileup2fq
lh3 is offline   Reply With Quote
Old 12-02-2009, 05:30 AM   #3
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Also try Galaxy

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

Works nicely
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