outliers

[Experimental] Identify outliers in bins relative to reference distributions.

Produces a table indicating sequences within genome bins that are outliers in either GC, tetranucleotide distance (TD), or coding density (CD) space relative to the expected distribution of these genomic statistics. The expected distribution was pre-calculated from reference genomes and the percentile used to identify outliers can be set with the -d flag (default = 95). Use -r to report sequences that are outliers in any (default) or all reference distributions.

This command requires the output folder of the analyze, lineage_wf, or taxonomy_wf command (results_dir) and a file indicating the tetranucleotide signature of all sequences within the genome bins. This file can be created with the tetra command. The output file can be passed to the modify command to remove the outlying sequences from a bin.

Arguments

usage: checkm outliers [-h] [-d dist_value] [-r {any,all}] [-x EXTENSION] [-q]
                       results_dir bin_input tetra_profile output_file

Identify outliers in bins relative to reference distributions.

positional arguments:
  results_dir           output directory of the analyze, lineage_wf or taxonomy_wf command (for marker_plot, qa must also have been run)
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  tetra_profile         tetranucleotide profiles for each sequence (see tetra command)
  output_file           print results to file

options:
  -h, --help            show this help message and exit
  -d, --distributions dist_value
                        reference distribution used to identify outliers; integer between 0 and 100 (default: 95)
  -r, --report_type {any,all}
                        report sequences that are outliers in 'all' or 'any' reference distribution (default: any)
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -q, --quiet           suppress console output

Example: checkm outliers ./output ./bins tetra.tsv outliers.tsv

Example

checkm tetra seqs.fna tetra.tsv
checkm outliers ./output ./bins tetra.tsv outliers.tsv