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KAPTIVE.PY(1) User Commands KAPTIVE.PY(1)

NAME - obtain information about K and O types for Klebsiella genome assemblies

SYNOPSIS [-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]


optional arguments:

show this help message and exit
Show Kaptive's version number and exit
FASTA file(s) for assemblies (default: None)
GenBank file with reference loci (default: None)
SRST2-formatted FASTA file of allelic typing genes to include in results (default: None)
Output directory/prefix (default: ./kaptive_results)
Display detailed information about each assembly in stdout (default: False)
The number of threads to use for the BLAST searches (default: 4)
Suppress output files of sequences matching locus (default: False)
Suppress output of tab-delimited table (default: False)
Suppress output of JSON file (default: False)
Missing bases at the ends of locus allowed in a perfect match. (default: 10)
minimum required % coverage for genes (default: 90.0)
minimum required % identity for genes (default: 80.0)
genes with a % identity below this value will be flagged as low identity (default: 95.0)
minimum locus matching assembly piece to return (default: 100)
when separate parts of the assembly are found within this distance, they will be merged (default: 100)
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)


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

September 2019 0.6.0