A pipeline for genomic variant detection with genome assemblies at population scale

Structural Variants ANnotator (SVAN)

TxGNN: Zero-shot prediction of therapeutic use with geometric deep learning and clinician centered design

Graph Neural Network Library for PyTorch

Working space for the GIAB TR benchmarking project

Python package for comparing genome assemblies and read data to the diploid Q100 benchmark

Genome In A Bottle Development Framework for Assembly Based Benchmarks

The Platinum Genomes Truthset

Reference-agnostic pipeline for generating Genome-in-a-Bottle stratifications

This repository contains a list of publications pertinent to the Genome in a Bottle project

TEtrimmer: a novel tool to automate manual curation of transposable elements

Haplotype VCF comparison tools

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

A complete diploid human genome

Pre-mAsking Long reads for Mobile Element inseRtion

Code written for the analyses found in the HGSVC3 manuscript.

L1ME-AID (L1 Mediated Annotation and Insertion Detector)

Project repository for the phase 3 main publication of the HGSVC

Methods to integrate data from multiple genome sequencing datasets and form consensus variant calls

Tool for plotting sequencing data along genomic coordinates.

This repository contains a list of tools or methods that have been used in GIAB analysis

This repository contains data indexes from NIST's Genome in a Bottle project.

Gfapy: a flexible and extensible software library for handling sequence graphs in Python

Code for hemitriccus pangenome project

Assembled Genomes Compressor

Pangenome structural variation (SV) merging and deduplication

code to analyse RepeatMasker output