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Old 11-22-2009, 09:26 PM   #1
julien
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Location: Raleigh NC

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Default Pileup to contig

Hi,
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 !!!!!
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Old 11-23-2009, 04:58 AM   #2
lh3
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samtools.pl pileup2fq
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Old 12-02-2009, 05:30 AM   #3
colindaven
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Default

Also try Galaxy

http://main.g2.bx.psu.edu/

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

Works nicely
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