.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH RESFINDER.PY "1" "November 2019" "resfinder.py 3.2" "User Commands"
.SH NAME
resfinder.py \- identify acquired antimicrobial resistance genes
.SH SYNOPSIS
.B resfinder.py
[\-h] \fB\-i\fR INPUTFILE [INPUTFILE ...] [\-o OUT_PATH]
[\-tmp TMP_DIR] [\-mp METHOD_PATH] [\-p DB_PATH]
[\-d DATABASES] [\-l MIN_COV] [\-t THRESHOLD]
[\-ao ACQ_OVERLAP] [\-matrix] [\-x] [\-q]
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-i\fR INPUTFILE [INPUTFILE ...], \fB\-\-inputfile\fR INPUTFILE [INPUTFILE ...]
FASTA or FASTQ input files.
.TP
\fB\-o\fR OUT_PATH, \fB\-\-outputPath\fR OUT_PATH
Path to blast output
.TP
\fB\-tmp\fR TMP_DIR, \fB\-\-tmp_dir\fR TMP_DIR
Temporary directory for storage of the results from
the external software.
.TP
\fB\-mp\fR METHOD_PATH, \fB\-\-methodPath\fR METHOD_PATH
Path to method to use (kma or blastn)
.TP
\fB\-p\fR DB_PATH, \fB\-\-databasePath\fR DB_PATH
Path to the databases
.TP
\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES
Databases chosen to search in \- if none are specified
all are used
.TP
\fB\-l\fR MIN_COV, \fB\-\-min_cov\fR MIN_COV
Minimum coverage
.TP
\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
Blast threshold for identity
.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\-matrix\fR, \fB\-\-matrix\fR
Gives the counts all all called bases at each position
in each mapped template. Columns are: reference base,
A count, C count, G count, T count, N count, \- count.
.TP
\fB\-x\fR, \fB\-\-extended_output\fR
Give extended output with alignment files, template
and query hits in fasta and a tab separated file with
gene profile results
.HP
\fB\-q\fR, \fB\-\-quiet\fR
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.