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