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README.md

CheckM

version status Bioconda Downloads BioConda Install

Installing and using CheckM

Please see the project home page for usage details and installation instructions: https://github.com/Ecogenomics/CheckM/wiki

We do not recommend installing CheckM from the master branch. This may be unstable. Please install an official release of CheckM or use pip.

Estimating quality of CPR genomes

Information about obtaining improved quality estimates for CPR (Patescibacteria) genomes can be found here: https://github.com/Ecogenomics/CheckM/wiki/Workflows#using-cpr-marker-set

Migration to Python 3

CheckM has been ported to Python 3 to accomodate Python 2 reaching end of life on January 1, 2020. CheckM >=1.1.0 requires Python 3. Python 2 will no longer be actively supported. Apologies for any issues this may cause.

Massive thanks to baudrly, Vini Salazar, and Asaf Peer for initial Python 2 to 3 porting.

Python 2 to 3 Validation

Porting of CheckM to Python 3 was validation on a set of 1,000 genomes randomly select from the GTDB R89 representative genomes. Results were compared to those generated with CheckM v1.0.18, the last Python 2 version of CheckM. Identical results were obtained for the 'lineage_wf', 'taxonomy_wf', and 'ssu_finder' methods across this set of test genomes. Other CheckM methods have been executed on a small set of 3 genomes to verify they run to completion under Python 3.

Removed Functionality

The following features have been removed from CheckM v1.1.x in order to simplify the code base and focus CheckM and support requests on critical functionality:

  • bin_qa_plot: non-critical, rarely used plot which does not scale to the large numbers of MAGs now being recovered
  • par_plot: non-critical plot and the same information is better presented in the reference distribution plots
  • cov_pca, tetra_pca: alternatives to these static plots exist in tools such as Anvi'o
  • len_plot: rarely used plot which is largely redundant with the len_hist and nx_plot plots
  • bin_union, bin_compare: feature rich alternative now exist such as DAS Tool and UniteM

Bug Reports

Please report bugs through the GitHub issues system.

Copyright © 2014 Donovan Parks, Connor Skennerton, Michael Imelfort. See LICENSE for further details.

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Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

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