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ggCaller is a novel bacterial gene annotation and pangenome analysis tool, designed to enable fast, accurate analysis of large single-species genome datasets.
ggCaller traverses de Bruijn graphs (DBGs) built by Bifrost, using temporal convolutional networks from Balrog for gene filtering and Panaroo for pangenome analysis and quality control.
Contents:
Why ggCaller?#
ggCaller uses population-frequency information at several stages of gene annotation and pangenome analysis. This has several benefits:
Consistent identification of start and stop codons across orthologs, improving clustering accuracy.
Reduced gene-annotation sensitivity to assembly fragmentation.
Reduced runtime verses existing gene-annotation and pangenome analysis workflows.
One-line command from fasta -> gene annotations, gene frequency matrices, clusters of orthologous genes (COGs), core genome/pangenome alignments, phylogenetic trees, small/structural variants and more!
Annotated DBG-querying for functional PanGenome-Wide Association Studies (PGWAS), compatible with results from Pyseer.
For the impatient#
See Quickstart to get ggCaller up and running quickly.
Everyone else#
We recommend starting with Installation to ensure things are installed correctly, followed by Usage to get an overview of the commands, and finally Tutorial for a step-by-step walkthrough.