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, --extented_output
              Give  extented  output with allignment files, template and query hits in fasta and a tab seperated
              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.

resfinder.py 3.2                                  November 2019                                  RESFINDER.PY(1)