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September 16, 2015 17:49
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Stream through qual & adapter trimming, 2pass Diginorm, split to /1 and /2 files.
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| interleave-reads.py file.1.fq.gz file.2.fq.gz \ | |
| | skewer -Q 2 -t 2 -x $HOME/Trimmomatic-0.33/adapters/TruSeq3-PE.fa - -1 \ | |
| | normalize-by-median.py --max-memory-usage 2e9 -C 30 -o - - \ | |
| | trim-low-abund.py -V -M 2e9 -o - --cutoff 2 - \ | |
| | split-paired-reads.py --output-orphaned orph.fq -1 stream.1.fq -2 stream.2.fq - |
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Er, sorry - I guess I don't get an email when comments happen. Skewer if a trimmomatic replacement. Better in that it can read/write from the stdin/stdout.