https://github.com/luntergroup/octopus

Bayesian haplotype-based mutation calling

bioinformatics de-novo-mutation genomics haplotypes phasing single-cell somatic-variants variant-calling variants

Last synced: 14 Jan 2026

https://github.com/mehelmy/princess

long-reads methylation phasing single-nucleotide-variation structural-variation

Last synced: 16 Jul 2025

https://github.com/fedarko/strainflye

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

bioinformatics metagenomics phasing variant-calling

Last synced: 19 Aug 2025

https://github.com/koesterlab/microphaser

phasing software variant-calling

Last synced: 28 Feb 2026

https://github.com/transbiozi/gimpute

An efficient genetic data imputation pipeline

genotyping gwas haplotypes imputation liftover phasing

Last synced: 03 Apr 2026

https://github.com/everestial/phase-stitcher

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

f1-hybrids genome-phasing haplotype-extension haplotypes phase-haplotypes phased-genotypes phasing population

Last synced: 18 Jan 2026

https://github.com/ai-sandbox/aegen

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

classification compression imputation phasing simulation

Last synced: 16 Jan 2026

https://github.com/deploid-dev/deploid-r

An R interface for 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.

cran deconvoluting-mixed-genomes hmm malaria mcmc parasites phasing unknown-proportions

Last synced: 07 Mar 2026