Commands

CheckM is executed from the command line and consists of a series of commands in order to support a number of different analyses and workflows. These commands are organized into several related groups, as listed by checkm -h. Help for each command can be shown with checkm <command> -h.

The two most common workflows are to assess genomes using either lineage-specific or taxonomic-specific marker sets (see Workflows).

Lineage-specific marker set

Taxonomic-specific marker set

Apply marker set to genome bins

analyze
qa

Common workflows

These workflows combine the above commands.

Plots

CheckM can produce a number of plots for assessing the quality of genome bins.

Reference distribution plots:

General plots:

Bin exploration and modification

Utility functions

CheckM also provides a number of additional commands that may be useful for exploring genome bins. Some of these commands also produce summary statistics of sequences required by specific plotting commands.

Reference data and testing

data
test

Removed commands

Commands removed in CheckM v1.1.x (e.g., bin_qa_plot, par_plot, cov_pca, tetra_pca, len_plot, bin_union, bin_compare, join_tables) are listed in Removed functionality.

checkm -h

                ...::: CheckM v1.3.0 :::...

  Lineage-specific marker set:
    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

  Taxonomic-specific marker set:
    taxon_list   -> List available taxonomic-specific marker sets
    taxon_set    -> Generate taxonomic-specific marker set

  Apply marker set to genome bins:
    analyze      -> Identify marker genes in bins
    qa           -> Assess bins for contamination and completeness

  Common workflows (combines above commands):
    lineage_wf   -> Runs tree, lineage_set, analyze, qa
    taxonomy_wf  -> Runs taxon_set, analyze, qa

  Reference distribution plots:
    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

  General plots:
    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     -> [Experimental] Identify outliers in bins relative to reference distributions
    modify       -> [Experimental] Modify sequences in a bin

  Utility functions:
    unbinned     -> Identify unbinned sequences
    coverage     -> Calculate coverage of sequences
    tetra        -> Calculate tetranucleotide signature of sequences
    profile      -> Calculate percentage of reads mapped to each bin
    ssu_finder   -> Identify SSU (16S/18S) rRNAs in sequences

  Testing:
    test         -> Run CheckM on a test genome (E. coli) to verify operation

  Use 'checkm data setRoot <checkm_data_dir>' to specify the location of CheckM database files.

  Usage: checkm <command> -h for command specific help