---
name: "kaptive.py"
section: "1"
platform: "linux"
package: "kaptive"
version: "2.0.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/kaptive.py"
---

# kaptive.py(1)

obtain information about K and O types for Klebsiella genome assemblies

## NAME

kaptive.py - obtain information about K and O types for Klebsiella genome assemblies

## SYNOPSIS

**kaptive.py** \[-h\] \[--version\] **-a** ASSEMBLY \[ASSEMBLY ...\] **-k** K\_REFS \[-g ALLELIC\_TYPING\] \[-o OUT\] \[-v\] \[-t THREADS\] \[--no\_seq\_out\] \[--no\_table\] \[--no\_json\] \[--start\_end\_margin START\_END\_MARGIN\] \[--min\_gene\_cov MIN\_GENE\_COV\] \[--min\_gene\_id MIN\_GENE\_ID\] \[--low\_gene\_id LOW\_GENE\_ID\] \[--min\_assembly\_piece MIN\_ASSEMBLY\_PIECE\] \[--gap\_fill\_size GAP\_FILL\_SIZE\] \[--locus\_label LOCUS\_LABEL\]

## OPTIONS

### 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)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.