Usage¶

Quickstart¶

gunc run -i genome.fa -r /path/to/db

This will run gunc on genome.fa with outputs going to the current working directory.

Main Commands¶

gunc run The main functionality of GUNC, runs chimerism detection.

gunc plot Produce an interactive plot using the output from gunc run

gunc merge_checkm Produce a merged file combining the outputs of GUNC and checkM

gunc download_db Download the GUNC database (required to run gunc run)

Any of the above commands can be run with -h to get function specific information.

GUNC accepts either a progenomes or GTDB based reference database via the --db_file option. Both can be downloaded using the gunc download_db command (see below). Note that using GTDB will lead to higher resource requirements and longer run times; in accuracy benchmarks, the performance of GTDB and the default proGenome-derived GUNC database performed very similarly.

GUNC RUN¶

Run chimerism detection.

Required Flags¶

--db_file Path to the GUNC database file. Can be set as environment variable GUNC_DB.

One of the following is required. If flag --gene_calls is not set gene calling will be done using prodigal with option “-p meta”.

--input_dir Input dir with files in FASTA format.

--input_file Input file containing paths to FASTA format files.

--file_suffix Only needed if suffix of input files is not the default .fa.

--input_fasta Input file in FASTA format.

Optional Flags¶

--gene_calls Input is FASTA faa format genecalls.

--use_species_level Allow species level to be picked as maxCSS. Default: False

--min_mapped_genes Dont calculate GUNC score if number of mapped genes is below this value. Default: 11

--threads Number of CPU threads.

--temp_dir Directory to store temporary files. Default: Current working directory.

--out_dir Directory in which to put output. Default: Current working directory.

--sensitive Run with high sensitivity. (Uses a different cutoff to determine an abundant lineage)

--detailed_output Output scores for every tax_level.

--contig_taxonomy_output Output taxonomic assignment for each contig.

GUNC PLOT¶

Create interactive plot to visualise chimerism.

Required Flags¶

--diamond_file GUNC diamond outputfile. (one of the output files in diamond_output produced by gunc run)

Optional Flags¶

--gunc_gene_count_file GUNC gene_counts.json file. (Not needed if --diamond file is in the file structure made by gunc run)

--out_dir Output directory. Default: Current working directory.

--tax_levels Tax levels to display (comma-seperated). (default: kingdom,phylum,family,genus,contig)

--remove_minor_clade_level Tax level at which to remove minor clades. (default: kingdom)

--contig_display_num Number of contigs to visualise. (default: 1000, 0 plots all contigs)

--contig_display_list Comma seperated list of contig names to plot.

GUNC MERGE_CHECKM¶

Merge outputs of GUNC and checkM. Both should have been run on the same input files. CheckM qa should be run with -f qa.tsv -o 2 --tab_table parameters. If run without -o 2 the extra columns will be empty.

Required Flags¶

--gunc_file Path of gunc_scores.tsv file.

--checkm_file CheckM output (qa.tsv) file (run checkm qa with -o 2 --tab_table parameters).

Optional Flags¶

--out_dir Output directory. Default: Current working directory.

GUNC DOWNLOAD_DB¶

Required Flags¶

positional argument Download database to given directory.

Optional Flags¶

--db Which db to download (progenomes or gtdb). Default: progenomes

Special Flags¶

--version Print version number and exit.

--help Print help message and exit.