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Old 02-03-2017, 08:24 AM   #59
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Tadpole is a purely kmer-based assembler, so by the time assembly is being done, there is no knowledge of which reads were used. Therefore, Tadpole can't provide that output. So, there are two ways to get it.

1) Map the reads to the assembly with BBMap and use the "outm" and "outu" flags to capture mapped and unmapped reads.
2) Use BBDuk to capture reads that share or do not share kmers with the assembly:

Code:
bbduk.sh in=reads.fq ref=contigs.fa k=31 mm=f out=unmatched.fq outm=matched.fq
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