Scripts used to perform analyses in Rice et al. (2023) "A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants."
This repository contains scripts used to perform analyses in the paper "A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.". It is divided into the following subdirectories, each with their own README:
genome-assembly: scripts used to assemble genomes to use to create the pangenomepangenome-creation: scripts used to create both the minigraph-cactus and PGGB pangenomespangenome-analysis: scripts for doing some calculations about the graph and its structurealignment-and-genotyping: scripts used to align reads to the pangenome and genotype based on those alignmentssimulation: scripts used to create simulated reads, align them to the pangenome with different methods, and compare the accuracy of the different alignmentsallele-balance: looking at reference bias based on allele balance
If you use any of the code in this repository in a manuscript, please cite the associated paper:
Rice et al. (2023). "A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants." BMC Biology 21:267. https://doi.org/10.1186/s12915-023-01758-0