[khmer] question re: trimmomatic/fastx

Fields, Christopher J cjfields at illinois.edu
Thu Feb 13 08:09:51 PST 2014

Apologies in advanced if this is known, but I couldn’t find the answer on the list.  Is there any reason behind why trimmomatic is being using only for adaptor trimming, whereas fastx is used for quality trimming?  We’ve usually done this in a single trimmomatic run, something like:

java -jar /usr/local/bin/trimmomatic-0.30.jar PE ../SRR492065_?.fastq.gz s1_pe s1_se s2_pe s2_se \
    ILLUMINACLIP:/usr/local/share/adapters/TruSeq3-PE.fa:2:30:10 \
    TRAILING:30 \
    LEADING:30 \


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