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Old 06-17-2014, 05:37 PM   #11
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by jimmybee View Post
Ive been using it over the last couple of weeks and it has been really quick. Im actually using it to run adapter trimming (with small inserts, all of your reads should overlap), so adding in some options for adapter matching would be handy (although I do know that you already have a trimming script in the bbtools suite)

I added some relevant flags and modes, in version 32.32. Thanks for the suggestions!

First, BBMerge now has a new flag, "tbo" (trimbyoverlap). Rather than joining reads, it will just trim the adapter sequence off the ends of reads that have an apparent insert size shorter than read length.

Second, I added the ability to overlap to BBDuk also, with the same flag, "tbo". So if you are trimming adapters fragment libraries with the normal read orientation, you can trim both by specifying an adapter sequence file and by overlap at the same time, which drastically reduces the false negative rate (reads that did not have adapters completely removed) by around a factor of 12. I highly recommend using both for fragment libraries, as the combination outperforms either one alone: in=reads.fq out=trimmed.fq tbo ktrim=r ref=truseq.fa k=25 mink=1 hdist=1

The 'tbo' flag is NOT recommended for long mate pair libraries which may have the adapters in totally different places and are not expected to overlap, which is why it is disabled by default.

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