Add fastp as option to check duplication levels
Example of fastp command on one sample :
paired_end :
fastp --in1 G0292_L001_R1.fastq.gz --in2 G0292_L001_R2.fastq.gz --out1 /net/beegfs/cfg/rundata/SequencingProjects/202309-016/analysis/fastp_G0292/G0292_L001_R1_fastp_filtered.fastq.gz --out2 /net/beegfs/cfg/rundata/SequencingProjects/202309-016/analysis/fastp_G0292/G0292_L001_R2_fastp_filtered.fastq.gz --overrepresentation_analysis --dup_calc_accuracy 5 --dedup 5 -R G0292 --html=/net/beegfs/cfg/rundata/SequencingProjects/202309-016/analysis/fastp_G0292/fastp_report_G0292.html --json=/net/beegfs/cfg/rundata/SequencingProjects/202309-016/analysis/fastp_G0292/fastp_report_G0292.json
Unpaired just remove --in2 and --out2
Memory needed : 12G (level 5 of duplication accuracy) Cores : 8 New conda package : fastp