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Old 12-04-2015, 09:58 PM   #25
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Hi Bob,

That's not possible with BBNorm, as it uses a lossy data structure called a count-min sketch to store counts. However, you can do that with KmerCountExact, which is faster than BBNorm, but less memory-efficient. Usage:

kmercountexact.sh in=reads.fq out=kmers.fasta


That will print them in fasta format; for 2-column tsv, add the flag "fastadump=f". There are also flags to suppress storing or printing of kmers with low counts.
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