CheckM

...::: CheckM v1.0.18 :::...

  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

  Bin QA plots:
    bin_qa_plot  -> Bar plot of bin completeness, contamination, and strain heterogeneity

  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_plot     -> Cumulative sequence length plot
    len_hist     -> Sequence length histogram
    marker_plot  -> Plot position of marker genes on sequences
    par_plot     -> Parallel coordinate plot of GC and coverage
    gc_bias_plot -> Plot bin coverage as a function of GC

  Sequence subspace plots:
    cov_pca      -> PCA plot of coverage profiles
    tetra_pca    -> PCA plot of tetranucleotide signatures

  Bin exploration and modification:
    unique       -> Ensure no sequences are assigned to multiple bins
    merge        -> Identify bins with complementary sets of marker genes
    bin_compare  -> Compare two sets of bins (e.g., from alternative binning methods)
    bin_union    -> [Experimental] Merge multiple binning efforts into a single bin set
    modify       -> [Experimental] Modify sequences in a bin
    outliers     -> [Experimental] Identify outlier in bins relative to reference distributions

  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
    join_tables  -> Join tab-separated value tables containing bin information
    ssu_finder   -> Identify SSU (16S/18S) rRNAs in sequences

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

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

...::: CheckM v1.0.18 :::... 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 Bin QA plots: bin_qa_plot -> Bar plot of bin completeness, contamination, and strain heterogeneity 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_plot -> Cumulative sequence length plot len_hist -> Sequence length histogram marker_plot -> Plot position of marker genes on sequences par_plot -> Parallel coordinate plot of GC and coverage gc_bias_plot -> Plot bin coverage as a function of GC Sequence subspace plots: cov_pca -> PCA plot of coverage profiles tetra_pca -> PCA plot of tetranucleotide signatures Bin exploration and modification: unique -> Ensure no sequences are assigned to multiple bins merge -> Identify bins with complementary sets of marker genes bin_compare -> Compare two sets of bins (e.g., from alternative binning methods) bin_union -> [Experimental] Merge multiple binning efforts into a single bin set modify -> [Experimental] Modify sequences in a bin outliers -> [Experimental] Identify outlier in bins relative to reference distributions 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 join_tables -> Join tab-separated value tables containing bin information ssu_finder -> Identify SSU (16S/18S) rRNAs in sequences Use 'checkm data setRoot <checkm_data_dir>' to specify the location of CheckM database files. Usage: checkm <command> -h for command specific help