modify

[Experimental] Modify sequences in a bin.

This is an experimental command that allows sequences to be added to (-a) or removed from (-r) a genome bin. It is also compatible with the outliers command: all sequences within a putative genome identified as outliers can be removed by passing the output of outliers with -o (this cannot be combined with -a or -r). Caution is warranted here as we have not explored the rate at which sequences identified as outliers do not belong in a genome bin.

Arguments

usage: checkm modify [-h] [-a ADD] [-r REMOVE] [-o OUTLIER_FILE] [-q]
                     seq_file bin_file output_file

Modify sequences in a bin.

positional arguments:
  seq_file              sequences used to generate bins (fasta format)
  bin_file              bin to be modified
  output_file           modified bin

options:
  -h, --help            show this help message and exit
  -a, --add ADD         ID of sequence to add to bin (may specify multiple times)
  -r, --remove REMOVE   ID of sequence to remove from bin (may specify multiple times)
  -o, --outlier_file OUTLIER_FILE
                        remove all sequences marked as outliers in the bin (see outlier command)
  -q, --quiet           suppress console output

Example: checkm modify -r seq_id1 -r seq_id2 seqs.fna bin.fna new_bin.fna

Example

checkm modify -r seq_id1 -r seq_id2 seqs.fna bin.fna new_bin.fna
checkm modify -o outliers.tsv seqs.fna bin.fna new_bin.fna