crux generate-peptides [options] <protein fasta file>


This command takes as input a protein FASTA file and outputs the corresponding list of peptides, as well as a matched list of decoy peptides and decoy proteins. Decoys are generated either by reversing or shuffling the non-terminal amino acids of each peptide. The program will shuffle each peptide multiple times to attempt to ensure that there is no overlap between the target and decoy peptides. For homopolymers, this is not possible. In this case, the occurrence of these target/decoy overlaps is recorded in the log file.

The program considers only the standard set of 20 amino acids. Peptides containing non-amino acid alphanumeric characters (BXZ) are skipped. Non-alphanumeric characters are ignored completely.



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: