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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
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Reference data is missing #370

Closed tiagocabralborelli closed 4 months ago

tiagocabralborelli commented 1 year ago

Hello Where can I find the universal reference genes data set to download?

donovan-h-parks commented 1 year ago

HMMs for the different marker sets used by CheckM can be found in the hmms directory of the CheckM reference data. Unfortunately, I don't think there is an easy way to get a particular set of marker genes. All HMMs are stored in a single file (phylo.hmm or checkm.hmm). You would need to extract the HMMs for the marker genes you are interested in.