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

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

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

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

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.

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

An add-on to floria for clustering reads into strains

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

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.