resfinder.py - identify acquired antimicrobial resistance
genes
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]
- -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
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.