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Old 09-20-2015, 12:03 PM   #6
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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JGI's reads are always interleaved like that. You can deinterleave them if you want like this (using the BBMap package):

reformat.sh in=reads.fq out1=read1.fq out2=read2.fq

...but that just makes all the commands longer, so I don't recommend it until you get to a tool that will not accept interleaved reads.

If you plan to merge the reads (which I am assuming you do, since they're 16S data) you can adapter-trim them first, but you don't really need to quality-trim first, and in fact it can reduce your merge rate. You can adapter-trim right adapters caused by short inserts using BBDuk like this:

bbduk.sh in=reads.fq out=trimmed.fq ref=adapters.fa tbo tpe ktrim=r hdist=1 k=23 mink=11

...but short inserts should not be very common in amplicon libraries unless you are targeting a region shorter than read length. There is a thread here discussing BBDuk options in more depth.

To merge the reads, I recommend BBMerge, like this:

bbmerge.sh in=reads.fq out=merged.fq outu=unmerged.fq qtrim2=r trimq=10

"qtrim2" will first try to merge the reads, then only do quality-trimming if merging is unsuccessful at first. This will result in a higher merge rate than quality-trimming first.
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