haplotype

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

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.

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

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

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

Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!

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

github repository for R package mpQTL

Joint inference of haplotypes and allele-specific expression from long-read bulk and single-cell RNA-seq

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

CHAP-GWAS: Chromosomal Haplotype-integrated GWAS

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

Haplotype phase information based genotype refinement tool

THESIAS: Testing Haplotype Effects In Association Studies

haplotype estimation, custom panel creation, and genotype imputation

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

A Haplotype-Resolved Transcriptome-Wide Association Framework.

haplotype viewer with bcftools-like selectors, C++ backend acceleration, and Python plotting.

（Internal testing）ONT read-level somatic-mutation integration for local mutation-state candidate analysis and methylation association; research software.

Java CLI for ranking Y-STR haplotypes and calculating TMRCA-related research metrics