optional arguments:

-h, --help

show this help message and exit

--version

Show Kaptive's version number and exit

-a ASSEMBLY [ASSEMBLY ...], --assembly ASSEMBLY [ASSEMBLY ...]

FASTA file(s) for assemblies (default: None)

-k K_REFS, --k_refs K_REFS

GenBank file with reference loci (default: None)

-g ALLELIC_TYPING, --allelic_typing ALLELIC_TYPING

SRST2-formatted FASTA file of allelic typing genes to include in results (default: None)

-o OUT, --out OUT

Output directory/prefix (default: ./kaptive_results)

-v, --verbose

Display detailed information about each assembly in stdout (default: False)

-t THREADS, --threads THREADS

The number of threads to use for the BLAST searches (default: 4)

--no_seq_out

Suppress output files of sequences matching locus (default: False)

--no_table

Suppress output of tab-delimited table (default: False)

--no_json

Suppress output of JSON file (default: False)

--start_end_margin START_END_MARGIN

Missing bases at the ends of locus allowed in a perfect match. (default: 10)

--min_gene_cov MIN_GENE_COV

minimum required % coverage for genes (default: 90.0)

--min_gene_id MIN_GENE_ID

minimum required % identity for genes (default: 80.0)

--low_gene_id LOW_GENE_ID

genes with a % identity below this value will be flagged as low identity (default: 95.0)

--min_assembly_piece MIN_ASSEMBLY_PIECE

minimum locus matching assembly piece to return (default: 100)

--gap_fill_size GAP_FILL_SIZE

when separate parts of the assembly are found within this distance, they will be merged (default: 100)

--locus_label LOCUS_LABEL

In the Genbank file, the source feature must have a note identifying the locus name, starting with this label followed by a colon (e.g. /note="K locus: K1") (default: automatically determined)