Pileup to contig

[julien]

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 !!!!!

[lh3]

samtools.pl pileup2fq

[colindaven]

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