A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi, I recently ran the pipeline to analyse faecal mouse samples. I was just wondering why Host-Read Removal is optional if it is supposed to improve performance and reduce false positive read assignment. In which cases or studies are you not supposed to know the host?

Many thanks for your answer!

Simple answer is that not every sample has a host - sediment or water or air metagenomes do not have a host

Furthermore some pipelines (e.g. clinical stuff) may already remove host DNA at sequencing during base calling, so it doesn't make sense to run it again.

And finally a lot of public data has host removed, so if you are reanalysing stuff also not necessary

Many Thanks James,
This clarifies me a lot for further analysis.

And just to specify in your case: it would make sense to host remove because mice are a model organism that probably has contaminated lots of reference genoems