phasing

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).

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

Ploidy agnostic phasing pipeline and algorithm

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

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.

GWAS QC, PCA, haplotype phasing, genotype imputation

An Example of Subgenome Phasing for Complex Allopolyploidy

Pipeline for analyzing rare mutations in metagenome-assembled genomes

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

A phasing and imputation pipeline for NGS data

scripts associated with yam genome assembly

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

An add-on to floria for clustering reads into strains

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

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

Microsatellite genotyping

A simple and efficient Python script for phasing long reads from a BAM file using a VCF file of phased heterozygous SNPs. The script assigns a haplotype (HP) tag to each read based on the alleles it carries at known SNP locations.