unique

Ensure no sequences are assigned to multiple bins.

Checks each putative genome and ensures no sequence has been assigned to multiple genomes. For most automated binning methods, the assignment of a sequence to multiple putative genomes would indicate a serious binning error. In practice, this command verifies that each sequence name is unique across all putative genomes.

Arguments

usage: checkm unique [-h] [-x EXTENSION] bin_input

Ensure no sequences are assigned to multiple bins.

positional arguments:
  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)]

options:
  -h, --help            show this help message and exit
  -x, --extension EXTENSION
                        extension of bins (all other files in bin directory are ignored) (default: fna)

Example: checkm unique ./bins

Example

checkm unique ./bins