.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH RUN_RESFINDER.PY "1" "July 2021" "run_resfinder.py 4.1.5" "User Commands"
.SH NAME
run_resfinder.py \- identify acquired antimicrobial resistance genes
.SH DESCRIPTION
usage: run_resfinder.py [\-h] [\-ifa INPUTFASTA]
.TP
[\-ifq INPUTFASTQ [INPUTFASTQ ...]] [\-o OUT_PATH]
[\-b BLAST_PATH] [\-k KMA_PATH] [\-s SPECIES]
[\-db_res DB_PATH_RES] [\-db_res_kma DB_PATH_RES_KMA]
[\-d DATABASES] [\-acq] [\-ao ACQ_OVERLAP] [\-l MIN_COV]
[\-t THRESHOLD] [\-c] [\-db_point DB_PATH_POINT]
[\-db_point_kma DB_PATH_POINT_KMA]
[\-g SPECIFIC_GENE [SPECIFIC_GENE ...]] [\-u]
[\-l_p MIN_COV_POINT] [\-t_p THRESHOLD_POINT] [\-\-pickle]
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-ifa\fR INPUTFASTA, \fB\-\-inputfasta\fR INPUTFASTA
Input fasta file.
.TP
\fB\-ifq\fR INPUTFASTQ [INPUTFASTQ ...], \fB\-\-inputfastq\fR INPUTFASTQ [INPUTFASTQ ...]
Input fastq file(s). Assumed to be single\-end fastq if
only one file is provided, and assumed to be pairedend data if two files are provided.
.TP
\fB\-o\fR OUT_PATH, \fB\-\-outputPath\fR OUT_PATH
Path to blast output
.TP
\fB\-b\fR BLAST_PATH, \fB\-\-blastPath\fR BLAST_PATH
Path to blastn
.TP
\fB\-k\fR KMA_PATH, \fB\-\-kmaPath\fR KMA_PATH
Path to KMA
.TP
\fB\-s\fR SPECIES, \fB\-\-species\fR SPECIES
Species in the sample
.TP
\fB\-db_res\fR DB_PATH_RES, \fB\-\-db_path_res\fR DB_PATH_RES
Path to the databases for ResFinder
.TP
\fB\-db_res_kma\fR DB_PATH_RES_KMA, \fB\-\-db_path_res_kma\fR DB_PATH_RES_KMA
Path to the ResFinder databases indexed with KMA.
Defaults to the 'kma_indexing' directory inside the
given database directory.
.TP
\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES
Databases chosen to search in \- if none is specified
all is used
.TP
\fB\-acq\fR, \fB\-\-acquired\fR
Run resfinder for acquired resistance genes
.TP
\fB\-ao\fR ACQ_OVERLAP, \fB\-\-acq_overlap\fR ACQ_OVERLAP
Genes are allowed to overlap this number of
nucleotides. Default: 30.
.TP
\fB\-l\fR MIN_COV, \fB\-\-min_cov\fR MIN_COV
Minimum (breadth\-of) coverage of ResFinder
.TP
\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
Threshold for identity of ResFinder
.TP
\fB\-c\fR, \fB\-\-point\fR
Run pointfinder for chromosomal mutations
.TP
\fB\-db_point\fR DB_PATH_POINT, \fB\-\-db_path_point\fR DB_PATH_POINT
Path to the databases for PointFinder
.TP
\fB\-db_point_kma\fR DB_PATH_POINT_KMA, \fB\-\-db_path_point_kma\fR DB_PATH_POINT_KMA
Path to the PointFinder databases indexed with KMA.
Defaults to the 'kma_indexing' directory inside the
given database directory.
.TP
\fB\-g\fR SPECIFIC_GENE [SPECIFIC_GENE ...]
Specify genes existing in the database to search for \-
if none is specified all genes are included in the
search.
.TP
\fB\-u\fR, \fB\-\-unknown_mut\fR
Show all mutations found even if in unknown to the
resistance database
.TP
\fB\-l_p\fR MIN_COV_POINT, \fB\-\-min_cov_point\fR MIN_COV_POINT
Minimum (breadth\-of) coverage of Pointfinder. If None
is selected, the minimum coverage of ResFinder will be
used.
.TP
\fB\-t_p\fR THRESHOLD_POINT, \fB\-\-threshold_point\fR THRESHOLD_POINT
Threshold for identity of Pointfinder. If None is
selected, the minimum coverage of ResFinder will be
used.
.TP
\fB\-\-pickle\fR
Create a pickle dump of the Isolate object. Currently
needed in the CGE webserver. Dependency and this
option is being removed.
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.