Thanks, I'll check out nf-core. Having a quick look there doesn't seem to be anything for analyzing Metagenomes with MEGAN but there looks like some interesting things I'm definitely interested in learning other tools down the line.
I think I was really treating it as a learning exercise to make sure I understood how all the steps of a pipeline fit together. Ideally, I'd also like to use my R1 and R2 data, and DIAMOND or is it meganizer only accepts one file as input.
what's the end goal? Is this metagenomics study?
Sorry I didn't mention that.
It's a metagenomics study, I'm looking to compare "Healthy" and dysbiotic microbiomes. The goal is to do Taxonomic and Functional Analysis.
In that case I would suggest biobakery pipelines as well.
Thank you, the HUMAnN pipeline looks really useful It looks like it does everything I'm interested in.
It looks like the pipeline takes only 1 file as input per sample, Are there any steps in my pre-processing I may have overlooked when trying to consolidate my data into a single fastq file.