HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

Segmented HAPlotype Estimation and Imputation Tool

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.

Using de-novo assembly and read-phasing to assemble reference-free diploid genomes

A tool to visualize the haplotype pattern and various information in excel.

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data.

Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.

This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato breeding“

github repository for R package mpQTL

gwas workflow from raw intensity data to in-silico functional mapping

THESIAS: Testing Haplotype Effects In Association Studies

haplotype estimation, custom panel creation, and genotype imputation

GWAS2: 2nd generation GWAS tool

*HaploCrackling* -- The Crackling-based method for variant-aware, whole-genome CRISPR-Cas9 target detection

Repository for running SeekDeep in a Docker Container

This is the data repository for the publication of the same name.

Y-DNA and mtDNA Haplotyping for WeGene, It features DFS algorithm and specific rules to search the most appropriate terminal haplotype based on haplogroup tree which should contain SNP information with position and derived mutation.

A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods

Programa Delfin 2022