CycloNovo is a new algorithm that identifies spectra generated from cyclopeptides in large mass spectrometry datasets. CycloNovo can also de novo sequence the cyclopeptides represented by identified cyclospectra. Latest betta version.

Developed in University of California San Diego, La Jolla, CA, USA

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:

 cyclonovo -s data/surugamide_spectrum.mgf -o test_output \
 --denovo -k 5 --verbosity -e 0.015 --kmer_threshold 2 

For the full list of available options please run

 cyclonovo -h

Output:

• cyclonovo_classification_report.txt: list spectra analyzed with scores related to identifying cyclospectra
• cyclonovo_cyclospectra.mgf: mgf file contaning found cyclospectra
• cyclonovo_sequencing_reconstructions.txt: reconstructions if de novo sequencing option is used

For the latest version and the web application see (GNPS account necessary): https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22CYCLONOVO%22%7D