bactopia-summary

Generate a summary table from the Bactopia results.

Usage

bactopia-summary [OPTIONS]

Required Options

Option	Type	Default	Description
--bactopia-path, -b	STRING		Directory where Bactopia results are stored

Gold Cutoffs

Option	Type	Default	Description
--gold-coverage, -gcov	INT	100	Minimum amount of coverage required for Gold status
--gold-quality, -gqual	INT	30	Minimum per-read mean quality score required for Gold status
--gold-read-length, -glen	INT	95	Minimum mean read length required for Gold status
--gold-contigs, -gcontigs	INT	100	Maximum contig count required for Gold status

Silver Cutoffs

Option	Type	Default	Description
--silver-coverage, -scov	INT	50	Minimum amount of coverage required for Silver status
--silver-quality, -squal	INT	20	Minimum per-read mean quality score required for Silver status
--silver-read-length, -slen	INT	75	Minimum mean read length required for Silver status
--silver-contigs, -scontigs	INT	200	Maximum contig count required for Silver status

Fail Cutoffs

Option	Type	Default	Description
--min-coverage, -mincov	INT	20	Minimum amount of coverage required to pass
--min-quality, -minqual	INT	12	Minimum per-read mean quality score required to pass
--min-read-length, -minlen	INT	49	Minimum mean read length required to pass
--max-contigs	INT	500	Maximum contig count required to pass
--min-assembled-size	INT		Minimum assembled genome size
--max-assembled-size	INT		Maximum assembled genome size

Additional Options

Option	Type	Default	Description
--outdir, -o	PATH	./	Directory to write output
--prefix, -p	STRING	bactopia	Prefix to use for output files
--force	BOOL	false	Overwrite existing reports
--verbose	BOOL	false	Print debug related text
--silent	BOOL	false	Only critical errors will be printed
--version, -V	BOOL	false	Show the version and exit.