I'm in charge of a genome assembly.
I have PE data and mate pair.
I usually perform a QC step with trimmomatic for my PE data.
However, I've never deal with mate pair ... does it has to be trimmed too ? which software can you recommend ?
See if this helps with mate pair question: http://seqanswers.com/forums/showthread.php?t=28951
These two things may be useful as well: http://www.illumina.com/documents/products/technotes/technote_nextera_matepair_data_processing.pdf and NxTrim.
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