merge

Identify bins with complementary sets of marker genes.

Identifies genome bins with complementary sets of marker genes. Merging such bins will result in a notable increase in completeness with only a marginal, or no, increase in contamination. Caution must be exercised before merging two bins.

To identify complementary sets of marker genes, a common set of markers must be sought in each bin, so this command requires a taxonomic-specific marker set (see taxon_set) or a HMM file of custom marker genes; lineage-specific marker files are not supported. We generally consider both the bacterial and archaeal sets produced by the taxon_set command.

It is entirely possible that two bins will have complementary sets of marker genes, but should not be merged. We have observed this situation many times. Additional information should be used to confirm the merging of bins. We only merge bins after verifying that they have similar genomic characteristics (e.g., GC, coverage) and are placed in similar locations within a reference genome tree. This information is available using the qa and tree_qa commands, respectively.

Pairs of bins meeting the --delta_comp, --delta_cont, --merged_comp, and --merged_cont criteria are written to <output_dir>/merger.tsv.

Arguments

usage: checkm merge [-h] [-g] [--delta_comp DELTA_COMP] [--delta_cont DELTA_CONT]
                    [--merged_comp MERGED_COMP] [--merged_cont MERGED_CONT] [-x EXTENSION]
                    [-t THREADS] [-q]
                    marker_file bin_input output_dir

Identify bins with complementary sets of marker genes.

positional arguments:
  marker_file           marker file to use for assessing potential bin mergers (marker set or HMM file)
  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)]
  output_dir            directory to write output files

options:
  -h, --help            show this help message and exit
  -g, --genes           bins contain genes as amino acids instead of nucleotide contigs
  --delta_comp DELTA_COMP
                        minimum increase in completeness to report pair (default: 5.0)
  --delta_cont DELTA_CONT
                        maximum increase in contamination to report pair (default: 10.0)
  --merged_comp MERGED_COMP
                        minimum merged completeness to report pair (default: 50.0)
  --merged_cont MERGED_CONT
                        maximum merged contamination to report pair (default: 20.0)
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -t, --threads THREADS
                        number of threads (default: 1)
  -q, --quiet           suppress console output

Example: checkm merge bacteria.ms ./bins ./output

Example

checkm taxon_set domain Bacteria bacteria.ms
checkm merge bacteria.ms ./bins ./output