Sickle/Scythe

Paired end

/data/CCRBioinfo/biowulf/local/sickle/sickle pe \
  -f <(/data/CCRBioinfo/biowulf/local/scythe/scythe -q sanger -a /data/CCRBioinfo/public/contaminants.fa <(gunzip -c ../staging/PATUXZ_RNA_Tumor_2077_1_1_63165AAXX.280_BUSTARD-2011-09-10.fq.gz)) \
  -r <(/data/CCRBioinfo/biowulf/local/scythe/scythe -q sanger -a /data/CCRBioinfo/public/contaminants.fa <(gunzip -c ../staging/PATUXZ_RNA_Tumor_2077_1_2_63165AAXX.280_BUSTARD-2011-09-10.fq.gz)) \
  -t sanger -o >(gzip > pe_PATUXZ_RNA_Tumor_2077_1_1_63165AAXX.280_BUSTARD-2011-09-10.trimmed.fq.gz ) \
  -p >( gzip > pe_PATUXZ_RNA_Tumor_2077_1_2_63165AAXX.280_BUSTARD-2011-09-10.trimmed.fq.gz ) \
  -s >( gzip > se_PATUXZ_RNA_Tumor_2077_1_1_63165AAXX.280_BUSTARD-2011-09-10.trimmed.fq.gz )

Single-end

./sickle se -f <(../scythe/scythe -a ../scythe/truseq_adapters.fasta -q sanger <(gunzip -c /data/CCRBioinfo/fastq/5_1_62EEFAAXX.213_BUSTARD-2011-02-19.fq.gz)) -t sanger -o trimmed.fq

Standalone Scythe

scythe -a /path/to/scythe/truseq_adapters.fasta -q sanger <(gunzip -c /data/CCRBioinfo/fastq/5_1_62EEFAAXX.213_BUSTARD-2011-02-19.fq.gz -o scythed.fq