.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH KAPTIVE.PY "1" "September 2019" "kaptive.py 0.6.0" "User Commands"
.SH NAME
kaptive.py \- obtain information about K and O types for Klebsiella genome assemblies
.SH SYNOPSIS
.B kaptive.py
[\-h] [\-\-version] \fB\-a\fR ASSEMBLY [ASSEMBLY ...] \fB\-k\fR 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]
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
Show Kaptive's version number and exit
.TP
\fB\-a\fR ASSEMBLY [ASSEMBLY ...], \fB\-\-assembly\fR ASSEMBLY [ASSEMBLY ...]
FASTA file(s) for assemblies (default: None)
.TP
\fB\-k\fR K_REFS, \fB\-\-k_refs\fR K_REFS
GenBank file with reference loci (default: None)
.TP
\fB\-g\fR ALLELIC_TYPING, \fB\-\-allelic_typing\fR ALLELIC_TYPING
SRST2\-formatted FASTA file of allelic typing genes to
include in results (default: None)
.TP
\fB\-o\fR OUT, \fB\-\-out\fR OUT
Output directory/prefix (default: ./kaptive_results)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Display detailed information about each assembly in
stdout (default: False)
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
The number of threads to use for the BLAST searches
(default: 4)
.TP
\fB\-\-no_seq_out\fR
Suppress output files of sequences matching locus
(default: False)
.TP
\fB\-\-no_table\fR
Suppress output of tab\-delimited table (default:
False)
.TP
\fB\-\-no_json\fR
Suppress output of JSON file (default: False)
.TP
\fB\-\-start_end_margin\fR START_END_MARGIN
Missing bases at the ends of locus allowed in a
perfect match. (default: 10)
.TP
\fB\-\-min_gene_cov\fR MIN_GENE_COV
minimum required % coverage for genes (default: 90.0)
.TP
\fB\-\-min_gene_id\fR MIN_GENE_ID
minimum required % identity for genes (default: 80.0)
.TP
\fB\-\-low_gene_id\fR LOW_GENE_ID
genes with a % identity below this value will be
flagged as low identity (default: 95.0)
.TP
\fB\-\-min_assembly_piece\fR MIN_ASSEMBLY_PIECE
minimum locus matching assembly piece to return
(default: 100)
.TP
\fB\-\-gap_fill_size\fR GAP_FILL_SIZE
when separate parts of the assembly are found within
this distance, they will be merged (default: 100)
.TP
\fB\-\-locus_label\fR 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)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.