Zhigui Bao's repositories
assembly-annotation-pipeline
Plant genome assembly and annotation pipeline using snakemake
Potato_C88
Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning
panEDTA-snakemake
Running panEDTA with snakmake
benchmarking-tools
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
genome-stratifications
Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium. These files can be used as standard resource of BED files for use with GA4GH benchmarking tools such as hap.py to stratify true positive, false positive, and false negative variant calls based on genomic context.
Haplotype-diversity
This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato breeding“
LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
singularity_def
Singularity definition files
vcfbub
use variant nesting information to flter overlapping sites from vg deconstruct output
wgatools
Whole Genome Alignment Tools