Microbial genomics pipeline to build and analyse genome graphs First version of best practice pipeline for use of graph genomes in microbial genomics, which include
- use whole genomes as input for constructing Pangenome graph, which encoded in the variation graph data model describe the all versus all alignment of many sequences
- manupilate the graph, such as annotation, visulaition and extract subregions
- map short reads to graph, get Gam files
- call variant using the Gam files either using genotying or including novel variants.
The variants called from graph based gam files can be used for further standard analysis as variants called from single linear reference.