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replace read end and quality trimming to use fastp #120
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But leave cutadapt for cleaning after kmc? I am not sure whether fastp can do the same as the number of reads after kmc is different and fastp does not like it. |
There is an incompatibility between fastp -i input/reads.pe1.fastq.gz -o tmp/reads.pe1.trimmed.fq --cut_front 4 --cut_front_mean_quality 10 -h tmp/reads.pe1.fastp.html
fastp -i input/reads.pe2.fastq.gz -o tmp/reads.pe2.trimmed.fq --cut_front 4 --cut_front_mean_quality 10 -h tmp/reads.pe1.fastp.html then after So, unless I am using fastp incorrectly, I would say we should stay with cutadapt at least for now. |
see the title...
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