phasing

zengxiaofei/HapHiC

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

MeHelmy/princess

HKU-BAL/ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

odelaneau/shapeit5

Segmented HAPlotype Estimation and Imputation Tool

PacificBiosciences/HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

zhangrengang/SubPhaser

Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.

everestial/VCF-Simplify

A python parser to simplify and build the VCF (Variant Call Format).

OmarOakheart/nPhase

Ploidy agnostic phasing pipeline and algorithm

Plant-Food-Research-Open/assemblyqc

A Nextflow pipeline for evaluating assembly quality

selfdecode/rd-imputation-accuracy

Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.4, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy metrics like: IQS(Imputation Quality score), r2 (Pearson correlation), Concordance.

DEploid-dev/DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

atgu/GWASpy

GWAS QC, PCA, haplotype phasing, genotype imputation

PacificBiosciences/minorseq

Minor Variant Calling and Phasing Tools

ptrebert/project-diploid-assembly

Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data

stjude/indelPost

Python library for simple and complex indels.

koesterlab/microphaser

transbioZI/Gimpute

An efficient genetic data imputation pipeline

BIGCS-Lab/phimtools

A phasing and imputation pipeline for NGS data

fedarko/strainFlye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

srubinacci/imputation-ukb-ref-panel

Genotype imputation pipelines for the UK Biobank Research Analysis Platform

victimofleisure/TripLight

psychedelic visual synthesizer color-organ style

bpucker/yam

scripts associated with yam genome assembly

everestial/phase-stitcher

a python program to stitch the ReadBack phased haplotypes in F1 hybrids.

dzhigaevd/phasor

Easy, fast, configurable version of phasor. Perfect for students who what to start with analyzing Coherent X-ray Diffraction Data.

RhettRautsaw/VariantCaller

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

acostauribe/TANGL

Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"

GeneMAP-Research/genemapgwas

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

AI-sandbox/aegen

Autoencoders for genomic data compression, classification, imputation, phasing and simulation.

everestial/PhaseIT

A pipeline for phasing haploptypes using short readbackphased haplotype blocks in population of samples.

everestial/SmallTools

Collection of several small tools. These tools stay here temporarily and may move to other major repositories as they evolve.

GeneMAP-Research/genemapimputationservice

haplotype estimation, custom panel creation, and genotype imputation

LauraSkak/Modification-count-workflow

This workflow uses Dorado, Samtools, Clair3, WhatHap and Modkit to extract a modification count table containing information for each relevant site.

maxibor/floria-strainer

An add-on to floria for clustering reads into strains

PengJia6/MSHunter

Microsatellite genotyping

plantformatics/phaseLD

LD-based phasing algorithm for segregating F1 populations (pseudo-oneway testcross)