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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
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Options or instructions for users with PE sequencing data #98

Closed LeandroRitter closed 1 year ago

LeandroRitter commented 1 year ago

Right now the workflow (due to aDNA traditions) is SE oriented. Typically users have PE data. The step of merging overlapping PE reads is not currently implemented (because in Anders' project all fastq-files were already merged by the aDNA SciLifeLab facility) but perhaps should be with e.g. fastp. Perhaps the whole Cutadapt step can be replaced with fastp?

LeandroRitter commented 1 year ago

I close it since we added some instructions about PE data to the README