haplotype
There are 19 repositories under haplotype topic.
zengxiaofei/HapHiC
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
odelaneau/shapeit5
Segmented HAPlotype Estimation and Imputation Tool
deepomicslab/SpecHLA
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.
Chenglin20170390/Haplotype-diversity
This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato breeding“
SAMtoBAM/PhasedDiploidGenomeAssemblyPipeline
Using de-novo assembly and read-phasing to assemble reference-free diploid genomes
cannin/snp_plotter
snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data.
fengcong3/HAPPE
A tool to visualize the haplotype pattern and various information in excel.
pdimens/harpy
Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.
alethere/mpQTL
github repository for R package mpQTL
GeneMAP-Research/genemapgwas
gwas workflow from raw intensity data to in-silico functional mapping
daissi/thesias
THESIAS: Testing Haplotype Effects In Association Studies
GeneMAP-Research/genemapimputationservice
haplotype estimation, custom panel creation, and genotype imputation
qj009/GWAS2
GWAS2: 2nd generation GWAS tool
bmds-lab/Crackling-phased
*HaploCrackling* -- The Crackling-based method for variant-aware, whole-genome CRISPR-Cas9 target detection
DanielRCA/NCR-mtDNA_ampliconbasedngs
A free and easy-to-use pipeline to analyse data from ancient NCR-mtDNA sequences obtained by amplicon-based NGS methods
roncuevas/Polymorphism
Programa Delfin 2022
zjwinn/Profiling-of-FHB-Resistance-QTL-Haplotypes-Through-MM-GBG-and-ML
This is the data repository for the publication of the same name.
colbyford/SeekDeep-Docker
Repository for running SeekDeep in a Docker Container
mahui-cn/weapp-haplotyping
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.