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cbirdlab / dDocentHPC

hard fork of dDocent, edited to run without interactive user input
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implement fastp instead of trimmomatic #12

Open cbird808 opened 3 years ago

cbird808 commented 3 years ago

fastp -i 20190905-PIRE-Ssp-A_P1P7-L4.F.fq.gz -I 20190905-PIRE-Ssp-A_P1P7-L4.R.fq.gz -o test_fastp-out/20190905-PIRE-Ssp-A_P1P7-L4.R1.fq.gz -O test_fastp-out/20190905-PIRE-Ssp-A_P1P7-L4.R2.fq.gz --compression 1 --verbose --detect_adapter_for_pe --cut_tail --cut_window_size 4 --cut_mean_quality 20 --length_required 75 --low_complexity_filter --complexity_threshold 30 --thread 40