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.