Ben J Woodcroft
Ben J Woodcroft
Thanks for the quick response - yes you are right about what I was after. And yes, CoverM can already do this (with `-m covered_fraction` or `covered_bases`). But as you...
fwiw the specific dataset is here, but it shows up for lots of (not tiny?) samples https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR7151488&display=metadata
We found it was faster for our particular use case (a quite small DB). Thanks for the fix.
Hi Javier, I wonder if this is an issue with your internet as connection or is temporary? -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT ________________________________ From: Javier...
Hmm. It's just a bit strange as I'm not having any issue downloading, at least the file from zenodo - haven't checked with checkm2 data.
A bit late here, but do you have any sense about whether removing shorter contigs before read mapping for binning changes the results in real world cases? Removing short contigs...
Sounds nice - does it have a conda? Might be easiest just to use the command line interface? How does it compare to skani?
Seems good now?
Pinned other stuff too - I guess that same logic applies. CI just broke, I think for unrelated reasons? I'm having trouble running tests locally due to HPC strangeness too.
Hi @rhysnewell or @AroneyS this good to go now?