Pileup to contig

julien

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Join Date: Nov 2009

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#1

Pileup to contig

11-22-2009, 10:26 PM

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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lh3

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#2

11-23-2009, 05:58 AM

samtools.pl pileup2fq
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colindaven

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#3

12-02-2009, 06:30 AM

Also try Galaxy

Galaxy

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

Galaxy is a community-driven web-based analysis platform for life science research.

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

Works nicely
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