15 months ago
University of Illinois Urbana-Champaign
If you are removing the Nextera internal adapter for mate-pair libraries, you should use NxTrim:
This will both trim the internal adapter and categorize the reads into groups: true mate-pairs, single-end, paired-end, and unknown (no adapter found, so likely a mix of true mates and paired-end). Note that the tool will revcomp the output by default to make them innies, which is NOT what most assemblers want. You can stifle this to keep the outie orientation by using the
Otherwise, the above choices will work for other standard adapter sequences.