NRPminer 1.0: Scalable Peptidogenomics Algorithm for Non-Ribosomal Peptide Discovery

IMPORTANT: this is the latest version of NRPminer that is going to be used in the GNPS web-application

NRPminer is a modification-tolerant scalable metabologenomics method for discovering NRPs by integrating (meta)genomics and tandem mass spectrometry (metabolomics) data

Dependencies (add binaries to PATH):

- NPDtools (https://github.com/ablab/npdtools)

System requirements:

- Linux or macOS
- Python 2.7
- GNU sed 

To configure/test run:

 make Makefile

Usage examples:

nrpminer.py -s [spectrum_file]  --antismash_resgbk [path_to_antiSMASH_generated_gbk] --orfDel [num_orfs_deleted] --derepdir [path_to_NPDtools_bin] --maxmod [maximum_modification_mass] -o [output_folder] --pvalue [pvalue_threshold] --threads [number of threads] --nrpspks_predictions_txt [path to SVM and CODE predictions folder]       

For the full list of available options please run

 nrpminer.py -h

Output:

** all_significant_psms.NRPminer.results.tsv :: list of all PSMs with significant PSM P-value as well as the sequence of the identified NRP