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annosine

SINE annotation tool for plant genomes

assembly-annotation-pipeline

Plant genome assembly and annotation pipeline using snakemake

benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

edta

Extensive de-novo TE Annotator

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.

panedta-snakemake

Running panEDTA with snakmake

phased-assembly-check

potato_c88

Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning

singularity_def

Singularity definition files

vcfbub

use variant nesting information to flter overlapping sites from vg deconstruct output

wfmash-paper

wgatools

Whole Genome Alignment Tools