run_resfinder.py - identify acquired antimicrobial resistance genes

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

run_resfinder.py 4.1.5                              July 2021                                RUN_RESFINDER.PY(1)

       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]

   optionalarguments:-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.

       run_resfinder.py - identify acquired antimicrobial resistance genes