Feedback on Workflow

Question

[01de]

Hello

I'm a PhD Student doing WGS for the first time and I was wondering if anyone could possibly offer some feedback on the pipeline I've put together. I have Paired-end Data which I would like to make the most of.

I'm not sure if I've made some glaring omissions or if any of these steps are redundant.

Any feedback would be greatly appreciated

[cpad0112]

what's the end goal? Is this metagenomics study?

[01de]

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.

[Asaf]

In that case I would suggest biobakery pipelines as well.

[01de]

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.

Answer 1

[Asaf]

There are already pipelines in place for everything these days. If this is your first time working with NGS and the sequencing is pretty standard I would suggest using those established pipelines. Take a look at nf-core

[01de]

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.