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Old 10-14-2015, 05:46 PM   #18
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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You can merge reads like this:

bbmerge-auto.sh in=reads.fq out=merged.fq outu=unmerged.fq ihist=ihist.txt extend2=20 iterations=10 k=31 ecct qtrim2=r trimq=12 strict

BBMerge will then attempt to merge each read pair. If unsuccessful, it will quality-trim the right end of each read to Q12, and try again (qtrim2=r trimq=12). If still unsuccessful, it will try to extend the reads by up to 20bp on the right end only, and try merging again, up to 10 times (extend2=20 iterations=10). This allows up to 200bp extension for each read, so that 2x250 reads can still merge even with an insert size approaching 900bp, near the limit of Illumina bridge-amplification. I recommend this over extending first then merging.

Note: The only difference between bbmerge.sh and bbmerge-auto.sh is that bbmerge.sh will try to grab a fixed amount of memory (because it doesn't need much) while bbmerge-auto.sh will try to grab all of the memory on the computer (because Tadpole will need it for storing the kmers).
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