Additional options

In case you are interested to skip STEP1 (Quality Control) please use option --skipQC. Please note that in this case low quality , low complexity and rRNA reads will not be filtered out. The input reads must be in the FASTA format (.fa or .fasta extension)

Please run ROP as follows:

python rop.py --skipQC example/test.fa example/ropOut60/

In case you are interested in unmapped reads with the reads from QC step to be filtered out, please use --dev option to save the afterQC.fastq.