Genome assembly and variant calling from PacBio HiFi reads

This folder contains two Snakemake workflows:

• assembly: from PacBio HiFi consensus reads to annotated genome assemblies
• variantcalling: combine assemblies into a pangenome graph and call variants from the graph

This is ongoing work, some things will change.

Requirements

Running the workflows requires Snakemake and Singularity. Both are installed on sciCORE and can be loaded as modules:

ml snakemake/6.6.1-foss-2021a 
ml Singularity/2.6.1

Section of a genome graph constructed from diverse MTBC genomes. It shows a nested structural variant: an IS6110 insertion within the TBD1 region.