Tag: nf-core

Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?

Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples? 0 Hi, I have some shotgun metagenomics gonorrhea samples and I want to use metagenomics pipeline to process the samples and then detect antimicrobial resistance. I looked into few pipelines so far for metagenomics data such as…

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How to pass custom software specific variables to nf-core/sarek nextflow pipeline?

How to pass custom software specific variables to nf-core/sarek nextflow pipeline? 0 I’m attempting to call whole genome variants using nf-core/sarek nextflow pipeline. In QC step there is an option that invokes trim_galore quality trimming, but i don’t know how to pass my custom adapters to be cut as well….

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