Ecogenomics / CheckM Public
Donovan Parks edited this page
Apr 9, 2022
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- About - What is CheckM?
- Citing - How can I cite CheckM?
- Contact Information - Who should I contact?
- Google Group - Post questions to the community!
- Contributors - People making CheckM better!
Bugs and Feature Requests
- Processing Large Numbers of Genomes - Process in batches!
- Bug Report - How can I report a bug?
- Feature Requests - How can I request a new feature?
- Known Issues - Are there any known issues?
The latest release of CheckM is v1.1.6 (April9, 2022). CheckM >=1.1.0 requires Python 3.
- System Requirements - What sort of computer is required to run CheckM?
- Installation - How can I install CheckM?
- Upgrade - How can I upgrade CheckM to the latest release?
- Unit Tests - How can I test my CheckM installation?
- KBase - CheckM is available online through KBase!
- Typical Workflow - What is the typical workflow for CheckM?
- Example Usage - How do I run CheckM?
Command Line Overview
- Overview - list of all CheckM features
- Lineage-specific Workflow - quality estimates with lineage-specific markers
- Taxonomic-specific Workflow - quality estimates with taxonomic-specific markers
- Using Custom Marker Genes - genome quality estimates with custom markers
- Using CPR Marker Set - genome quality estimates with a CPR/Patescibacteria specific marker set
Genome Quality Commands
- tree - place bins in the reference genome tree
- tree_qa - assess phylogenetic markers found in each bin
- lineage_set - infer lineage-specific marker sets for each bin
- taxon_list - list available taxonomic-specific marker sets
- taxon_set - infer taxonomic-specific marker set
- analyze - identify marker genes in bins
- qa - assess bins for contamination and completeness
- gc_plot - create GC histogram and delta-GC plot
- coding_plot - create coding density (CD) histogram and delta-CD plot
- tetra_plot - create tetranucleotide distance (TD) histogram and delta-TD plot
- dist_plot - create image with GC, CD, and TD distribution plots together
- nx_plot - create Nx-plots
- len_hist - sequence length histogram
- marker_plot - plot position of marker genes on sequences
- gc_bias_plot - plot bin coverage as a function of GC
Bin Exploration and Modification
- unique - ensure no sequences are assigned to multiple bins
- merge - identify bins with complementary sets of marker genes
- outliers - identify outliers in bins relative to reference distributions
- modify - modify sequences in a bin
- unbinned - identify unbinned sequences
- coverage - calculate coverage of sequences
- tetra - calculate tetranucleotide signature of sequences
- profile - calculate percentage of reads mapped to each bin
- join_tables - join tab-separated value tables containing bin information
- ssu_finder - identify SSU (16S/18S) rRNAs in sequences