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

nf-core

Adding another thread here for clarity — has anyone done a deep dive into host depletion?  This might be a good standalone topic for the hackathon

There have been a flurry of tools published I haven’t tried yet, and <https://www.nature.com/articles/s41564-023-01381-3|this paper> provides a nice framework for checking how well they actually work (for anonymizing, at least).  It would be great to have a CAMI-style effort to score host removal methods to see whats going to be best.

Just seeing this actually! <https://www.biorxiv.org/content/10.1101/2025.03.27.645632v1.full>

We have a whole pipeline for it <#C06316EFZSQ|> :grimacing:

Also we've added or started to add a bunch of tools like hostile or deacon

But most of the tools that benchmark themselves often find a very small difference