Bayesian haplotype-based mutation calling

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

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

Segmented HAPlotype Estimation and Imputation Tool

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

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

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

Ploidy agnostic phasing pipeline and algorithm

A Nextflow pipeline for evaluating assembly quality

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 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.

A bioinformatics pipeline to phase and impute genetic data

GWAS QC, PCA, haplotype phasing, genotype imputation

Minor Variant Calling and Phasing Tools

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

Phasing and scaffolding polyploid genomes based on Pore-C or Hi-C.

Python library for simple and complex indels.

An efficient genetic data imputation pipeline