The NCBI_pathogen_prospector is an tool for the automated download and subsequent analysis of fasta-files from NCBI pathogen using the assembly accession-numbers. The analysing-steps include ABRicate (https://github.com/tseemann/abricate) and a filtering for carbapenemases-genes. As separate function included is the automated download of MIC-data from NCBI biosample via the biosample accession-numbers.
NCBI_pathogen_prospector requires the following programs on your system to run:
- nextflow
- install nextflow to your system (https://www.nextflow.io/)
- clone this git-repository to your computer using the command:
git clone https://github.com/DataSpott/NCBI_pathogen_prospector.git- use the following command to show the help-message:
path/to/NCBI_pathogen_prospector/main.nf --help- create a list of assembly accenssion-numbers & save it to a file (no header, one number per line)
- hand the list-file to the assembly_nrs-flag:
path/to/NCBI_pathogen_prospector/main.nf --assembly_nrs path/to/assmebly_nr_list.file- due to limitations in the download-rate from NCBI the maximum amount of processes at the same time is limited to two for the fasta-download-process.
- If you posses an NCBI API-key you can use the api_key-flag to increase the amount of simultaneous fasta-downloads to 5:
path/to/NCBI_pathogen_prospector/main.nf --assembly_nrs path/to/assmebly_nr_list.file --api_key "your_api_key"