Is there a possibility to have the distance between the putative genome and the closest reference genome?

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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Is there a possibility to have the distance between the putative genome and the closest reference genome? #363

Closed dgrissa closed 4 months ago

dgrissa commented 1 year ago

As part of my research work, I would like to know the different reasons for having genomes with bad scores for completeness usng CheckM. For that, I would like to know the distance between the putative genome and the closest reference genome. Would that be possible or easy to compute? Thank you in advance for your answer.

donovan-h-parks commented 1 year ago

CheckM v1 is no longer in active development. I believe the CheckM output contains a Newick tree with your genomes as placed using pplacer. You should be able to pull the information from this tree though I don't know a program that can generate the exact information you are after.