The results of CheckM analysis of a genome are available for viewing in the new version of NCBI Datasets, i.e. genome completeness and contamination. If I now wish to bulk download a batch of genome checkm results, how do I accomplish this?
I emailed NCBI Feedback and recently received a response. The main contents are as follows.
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We are planning to add CheckM data to our genome table pages (for example, https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=255045) in the coming months.
In the meantime, there are two ways you can obtain CheckM analysis results: 1) using the NCBI Datasets command line tools or 2) downloading all CheckM data from FTP.
To get CheckM analysis results using the NCBI Datasets command line tools, try the following command:
datasets summary genome taxon 255045 --as-json-lines | \
dataformat tsv genome --fields organism-name,accession,checkm-completeness,checkm-contamination | \
head -5
Organism Name Assembly Accession CheckM completeness CheckM contamination
Bradyrhizobium canariense GCF_019402665.1 97.08 0.16
Bradyrhizobium canariense GCF_002108675.1 99.39 0.45
Bradyrhizobium canariense GCF_002108695.1 99.1 0.45
Bradyrhizobium canariense GCF_002108725.1 99.39 0.69
Alternatively, you can just download all CheckM analysis data by downloading the following file from FTP:https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/CheckM_report_prokaryotes.txt
K-Base also has the provision to run CheckM for bacterial genomes. You can check this out:
https://kbase.us/applist/apps/kb_Msuite/run_checkM_lineage_wf/release#:~:text=CheckM%20provides%20a%20set%20of,copy%20within%20a%20phylogenetic%20lineage.
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