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Old 12-12-2016, 05:20 PM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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There are three primary ways. I'll describe how to do them using the BBMap package.

1) Via mapping, which requires a reference:
bbmap.sh in1=r1.fastq in2=r2.fastq ref=ref.fasta ihist=ihist.txt reads=2m pairlen=2000

2) Via overlap, which requires overlapping reads (they probably overlap given you ran at 2x250):
bbmerge.sh in1=r1.fastq in2=r2.fastq ihist=ihist.txt reads=2m

3) Via assembly, which requires sufficient read depth and memory to assemble the genome:
bbmerge-auto.sh in1=r1.fastq in2=r2.fastq ihist=ihist.txt extend2=200

2 is the fastest. The best choice and best settings depend on your data, though. Can you describe the organism, experiment, and target insert size?
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