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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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Understanding contamination value #374

Closed stephane-wang closed 1 year ago

stephane-wang commented 1 year ago

Hi,

I am working on raw bacterial reads and I did de-novo genome assembly on my raw reads and I wanted to assess the quality of my assemblies with CheckM. So I ran lineage_wf on my dataset but some of the genomes show a level contamination above 100%, one even has a level contamination of ~480%. And would like to understand this value.

Thanks for your help.

ramay commented 1 year ago

Hi, I am having the same issue! Can someone please explain why the contamination percent can be > 100.

Thanks! Hena

ramay commented 1 year ago

I found an issue where it is explained https://github.com/Ecogenomics/CheckM/issues/318