NAME

       run_resfinder.py - identify acquired antimicrobial resistance genes

DESCRIPTION

       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]

   optional arguments:
       -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.

AUTHOR

        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)