#76 dupedist value for AVITI machine

[Assa Yeroslaviz]

Thanks for a great tool.

I was wondering how the value fordupedist=40 was set?
In the help page you have a list of different illumina machine. I assume the values differ due to the different flowcells used in the sequencing and the distances between clusters to identify optical duplicates? Is this correct?

I would like to know if you can modify the help page to also add values for other machines such as the AVITI machine we are using for sequencing?

thank

[Assa Yeroslaviz]

I'm asking because I can see very different results in the read number of duplicated reads when checking a specific file. When running it with fatqc I get over 90% duplications, when using fastp to calculate duplications I have only 47.3% duplicated reads, but when testing it with clumpify I get 0.213% duplication rate.

I can't explain these differences, unless I'm using the wrong parameters for searching duplications.

The commands for the two tools are as followed:

  fastp --in1 ${prefix}${file}_R1.fastq.gz \
        --in2 ${prefix}${file}_R2.fastq.gz \
        --thread 16 \
        -p -P 20 \
        --dedup --dup_calc_accuracy 5 \
        --qualified_quality_phred 15 \
        --unqualified_percent_limit 40 \
        --length_required 15 \
        --detect_adapter_for_pe   \
        --out1 fastpResults/${file}.trimmed.R1.fq.gz \
        --out2 fastpResults/${file}.trimmed.R2.fq.gz 

clumpify.sh -Xmx20g in=rawdata/s46_R1.fastq.gz in2=rawdata/s46_R2.fastq.gz \
            out=clumpify_runs/s46_R1_clumped.fq.gz out=s46_R2_clumped.fq.gz \
            dedupe=t optical=t addcount=t