unbinned

Identify unbinned sequences.

Given a set of genome bins along with a FASTA file of sequences, determines which of these sequences are not currently contained in a genome bin. This is useful for determining which sequences from an assembly were not binned by an automated binning algorithm. The unbinned sequences are written to a FASTA file and their length and GC to a tab-separated statistics file.

Arguments

usage: checkm unbinned [-h] [-x EXTENSION] [-s MIN_SEQ_LEN] [-q]
                       bin_input seq_file output_seq_file output_stats_file

Identify unbinned sequences.

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)]
  seq_file              sequences used to generate bins (fasta format)
  output_seq_file       write unbinned sequences to file
  output_stats_file     write unbinned sequence statistics to file

options:
  -h, --help            show this help message and exit
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -s, --min_seq_len MIN_SEQ_LEN
                        required length of sequence
  -q, --quiet           suppress console output

Example: checkm unbinned ./bins seqs.fna unbinned.fna unbinned_stats.tsv

Example

checkm unbinned ./bins seqs.fna unbinned.fna unbinned_stats.tsv