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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
347 stars 73 forks source link

Checkm data still available? #362

Closed standage closed 1 year ago

standage commented 1 year ago

Greetings!

I am unable to resolve https://data.ace.uq.edu.au/public/CheckM_databases/ in my web browser nor the tarball URL from the command line with curl/wget. Is this resource still live? Is there any way a copy of this data can be deposited in a legit archive such as figshare or zenodo?

donovan-h-parks commented 1 year ago

Should be up again now.

standage commented 1 year ago

Can confirm. Thanks!

(My suggestion regarding depositing the file in a reliable public archive still stands. Uptime aside, academic websites are notorious victims to department reorganizations, P.I. relocations, and so on.)

donovan-h-parks commented 1 year ago

CheckM reference data has been placed on Zenodo: https://zenodo.org/record/7401545#.Y44ymHbMJD8

azat-badretdin commented 1 year ago

Any plans to update the reference set? There are some major changes in NCBI Taxonomy reflecting the global Taxonomy changes and it would be nice to have up to date taxonomically correct marker set...

donovan-h-parks commented 1 year ago

CheckM v1 is no longer actively updated. Development effort is now on CheckM v2 that uses a machine learning approach to estimate genome quality: https://www.biorxiv.org/content/10.1101/2022.07.11.499243v1.

azat-badretdin commented 1 year ago

Thanks, we will take a look

standage commented 1 year ago

CheckM reference data has been placed on Zenodo

Fantastic. Thank you!