I'm interested in generating a fasta file from Ilumina paired reads of my wild 
type strain. I have an NCBI reference genome I can assemble against and I have 
already uploaded my 2 reads (using the NCBI reference as my genome), used fastq 
groomer, aligned them with bowtie and generated my pileup.

What I think I want to do though is to extract from the pileup a consensus 
fasta file (using 20 or something as a quality cutoff threshold) and then used 
that as my new reference genome to align 2 mutant strains against that are from 
that genetic background. How can I do that in Galaxy? I don't see any way to go 
from pileup to fastaq or pileup to fasta using some sort of cutoff. I think I 
can use samtools pileup2fq based on web posts (and then used something else to 
make a fasta file), but I would like to do all my analysis in galaxy.

Is this possible?

Any help appreciated, I am new with Galaxy.

 -John
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