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.

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)