RUN_RESFINDER.PY

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.