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Old 05-28-2014, 08:44 AM   #45
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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BBTools has a tool to quickly re-pair arbitrarily disordered reads based on their names.

For interleaved reads:

repair.sh in=reads.fq out=fixed.fq outsingle=single.fq

For paired reads in two files:

repair.sh in1=read1.fq in2=read2.fq out1=fixed1.fq out2=fixed2.fq outsingle=single.fq

You can also repair simple broken interleaving much faster and with less memory, but this will not fix arbitrarily disordered reads, just reads that were interleaved and had some of the reads thrown away:

bbsplitpairs.sh in=reads.fq out=fixed.fq outsingle=single.fq fixinterleaving

Last edited by Brian Bushnell; 02-13-2015 at 10:31 AM.
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