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.

kaptive.py 0.6.0                                 September 2019                                    KAPTIVE.PY(1)