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.
Traversal and gene-calling cut-off settings¶
--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)
Avoid/include algorithms¶
--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)--no-clustering
: Do not cluster ORFs (Default = False)--no-refind
: Do not refind missed genes (Default = False)
Gene clustering options¶
--identity-cutoff
: Minimum identity at amino acid level between two ORFs for lowest-level clustering (Default = 0.98)--len-diff-cutoff
: Minimum ratio of length between two ORFs for lowest-level clustering (Default = 0.98)--family-threshold
: Gene family sequence identity threshold (default=0.7)--merge-paralogs
: Don’t split paralogs during Panaroo quality control (Default = False)
Annotation options¶
--evalue
: Maximum e-value to return for DIAMOND and HMMER searches during annotation (Default = 0.001)--truncation-threshold
: Sequences in a cluster less than centroid length * truncation-threshold will be annotated as ‘potential pseudogene’ (Default = 0.8)
Gene-refinding options¶
--search-radius
: The distance (bp) surrounding the neighbour of an accessory gene in which to search for it (Default = 5000)--refind-prop-match
: The proportion of an accessory gene’s length that must be found in order to consider it a match (Default = 0.2)
Gene graph correction stringency options (determined by clean-mode)¶
--min-trailing-support
: Minimum cluster size to keep a gene called at the end of a contig.--trailing-recursive
: Number of times to perform recursive trimming of low support nodes near the end of contigs--edge-support-threshold
: Minimum support required to keep an edge that has been flagged as a possible mis-assembly--length-outlier-support-proportion
: Proportion of genomes supporting a spurious long gene (>1.5x outside the IQR of cluster)--min-edge-support-sv
: Minimum edge support required to call structural variants in the presence/absence sv file--no-clean-edges
: Turn off edge filtering in the final output graph
Alignment options¶
--no-variants
: Do not call variants using SNP-sites after alignment (Default = False)--ignore-pseduogenes
: Ignore ORFs annotated as ‘potential pseudogenes’ in alignments (Default = False)
Misc. options¶
--quiet
: Suppress additional output to console (Default = False)--version
: Show program’s version number and exit (Default = False)