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Sep 18th, 2019
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  1. mkdir -p {params.outdir}
  2. /lustre1/ctgb-usr/local/src/bbmap/bbduk.sh \
  3. -Xmx14g \
  4. in={input.R1} in2={input.R2} \
  5. out={output.R1} out2={output.R2} \
  6. ref=/lustre1/genomes/Illumina_Adapters/BBDUK/adapters.fa \
  7. k=23 mink=11 rcomp=t ktrim=f kmask=X qtrim=rl trimq=5 \
  8. forcetrimleft=2 forcetrimright2=2 overwrite=true
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