NAME
resfinder.py - identify acquired antimicrobial resistance genes
SYNOPSIS
resfinder.py [-h] -i 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]
OPTIONS
optional arguments:
- -h, --help
-
show this help message and exit
- -i INPUTFILE [INPUTFILE ...], --inputfile INPUTFILE [INPUTFILE ...]
-
FASTA or FASTQ input files.
- -o OUT_PATH, --outputPath OUT_PATH
-
Path to blast output
- -tmp TMP_DIR, --tmp_dir TMP_DIR
-
Temporary directory for storage of the results from the external software.
- -mp METHOD_PATH, --methodPath METHOD_PATH
-
Path to method to use (kma or blastn)
- -p DB_PATH, --databasePath DB_PATH
-
Path to the databases
- -d DATABASES, --databases DATABASES
-
Databases chosen to search in - if none are specified all are used
- -l MIN_COV, --min_cov MIN_COV
-
Minimum coverage
- -t THRESHOLD, --threshold THRESHOLD
-
Blast threshold for identity
- -ao ACQ_OVERLAP, --acq_overlap ACQ_OVERLAP
-
Genes are allowed to overlap this number of nucleotides. Default: 30.
- -matrix, --matrix
-
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.
- -x, --extended_output
-
Give extended output with alignment files, template and query hits in fasta and a tab separated file with gene profile results
-q, --quiet
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.