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- Command line interface
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- GNU General Public License version 2.0
- Donovan H. Parks <>
No open topic.
(Parks et al., 2015)
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
PMID: 25977477 DOI: 10.1101/gr.186072.114
Australian Centre for Ecogenomics, School of Chemistry & Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia; Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland, Australia
1 user review
1 user review
I have found this tool extremely useful for evaluating bins created by various binning tools (MetaBAT, MaxBin, and MyCC are the ones I've used the most). It's very good for getting a preliminary overview of how "good" the bins and sometimes for assigning bins to specific taxa. (I'm working with fairly complex environmental samples, so often my bins will be fairly incomplete/contaminated, and cannot be assigned at the family/genus/species levels.)
Installation can be somewhat challenging, because the tool has a fair number of dependencies that need to be installed as well. Ultimately, I chose to install it on a virtual machine running a 64 bit version of Ubuntu; I could perform most of the basic functions there, but didn't have enough RAM for some of the more computationally-intensive functions (for example, tetra, which calculates the tetranucleotide signatures).
I find the "bin_qa_plot" very useful to asses bins at a glance, and there are a variety of other useful graphical outputs to look more closely at the coverage and composition of individual bin. The tool also offers a number of ways to modify and refine bins manually, and the combination has the potential to be very powerful in recovering more complete draft genomes from metagenomes.
The tool can also be used to evaluate the results of single-cell genomics or genomes recovered from isolates, so it has broader applications than just metagenomics.