Advanced¶

For advanced users, ggCaller has a number of parameters for altering gene prediction, annotation and quality control.

Input/output¶

--kmer: value of k used to build Bifrost DBG (Default and max value = 31).
--all-seq-in-graph: Output gene graph GML file with all DNA and amino acid sequences. Off by default due to large file size.
--balrog-db: Path to an existing download of the balrog annotation database. If this does not exist, downloaded and placed in path for future use.
--gene-finding-only: Only run ggCaller gene-finding and generate a gff compatible with other clustering tools.

--max-path-length: Maximum path length traversed during ORF finding (bp) (Default = 20000)
--min-orf-length: Minimum ORF length to return (bp) (Default = 90)
--score-tolerance: Probability threshold for shorter alternative start sites based on average stop codon frequency (Default = 0.2)
--max-ORF-overlap: Maximum overlap allowed between two ORFs (bp) (Default = 60)
--min-path-score: Minimum total BALROG score for a maximum tiling path of ORFs to be returned (Default = 100)
--min-orf-score: Minimum individual Balrog score for an ORF to be returned (Default = 100)
--max-orf-orf-distance: Maximum distance between two ORFs to be connected (bp) (Default = 10000)

--no-filter: Do not filter ORF calls using Balrog, will return all ORF calls (Default = False)
--no-write-idx: Do not write FMIndexes to file (Default = False)
--no-write-graph: Do not write Bifrost GFA and colours to file (Default = False)
--repeat: Enable traversal of nodes multiple times, only applicable when DBG built from reads (Default = False)