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

       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)

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

optionalarguments:-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)

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]