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o-william-white / skim2mito

A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from genome skims
MIT License
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Add option to activate deduplication with fastp #10

Closed martinstervander closed 1 year ago

martinstervander commented 1 year ago

Add option to pass argument "--dedup" to fastp, in order to activate deduplication of reads. This is important both to not waste computational resources and to get a result in which the coverage is informative, and not inflated by PCR copies. This will be particularly important for hDNA/aDNA.

o-william-white commented 1 year ago

Option added to config file :) Thanks @martinstervander, hope you are well!