phasing

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 tumor–normal pair somatic small variant calling

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C, Omni-C).

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

A bioinformatics pipeline to phase and impute genetic data

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.

GWAS QC, PCA, haplotype phasing, genotype imputation

An Example of Subgenome Phasing for Complex Allopolyploidy

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

Minor Variant Calling and Phasing Tools

Haplotype-aware assembly of complex regions and small genomes

Python library for simple and complex indels.

An efficient genetic data imputation pipeline