phasing
There are 0 repository under phasing topic.
luntergroup / octopus
Bayesian haplotype-based mutation calling
Language:C++ 310zengxiaofei / HapHiC
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
Language:Python 228- Language:Python 93
- Language:Python 81
- HiPhase
PacificBiosciences / HiPhase
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
Language:Rust 78 - Language:C++ 77
zhangrengang / SubPhaser
To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
Language:Python 66wangyibin / CPhasing
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
Language:Python 57everestial / VCF-Simplify
A python parser to simplify and build the VCF (Variant Call Format).
Language:Python 49OmarOakheart / nPhase
Ploidy agnostic phasing pipeline and algorithm
Language:Python 47Plant-Food-Research-Open / assemblyqc
A Nextflow pipeline for evaluating assembly quality
Language:Nextflow 33nf-core / phaseimpute
A bioinformatics pipeline to phase and impute genetic data
Language:Nextflow 22selfdecode / rd-imputation-accuracy
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.
Language:Python 22DEploid-dev / 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.
Language:C++ 20- Language:Python 18
ptrebert / project-diploid-assembly
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
Language:Jupyter Notebook 16Minor Variant Calling and Phasing Tools
- Language:C 13
- Language:Rust 12
fedarko / strainFlye
Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
Language:Python 11srubinacci / imputation-ukb-ref-panel
Genotype imputation pipelines for the UK Biobank Research Analysis Platform
Language:Shell 11transbioZI / Gimpute
An efficient genetic data imputation pipeline
Language:R 11- Language:Python 8
- Language:Python 8
a python program to stitch the ReadBack phased haplotypes in F1 hybrids.
Language:Jupyter Notebook 8victimofleisure / TripLight
psychedelic visual synthesizer color-organ style
Language:C++ 8acostauribe / TANGL
Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"
Language:Shell 4AI-sandbox / aegen
Autoencoders for genomic data compression, classification, imputation, phasing and simulation.
Language:Python 4dzhigaevd / phasor
Easy, fast, configurable version of phasor. Perfect for students who what to start with analyzing Coherent X-ray Diffraction Data.
Language:MATLAB 4bluenote-1577 / dbghaplo
Long-read haplotyping of small sequences with SNP-encoded de Bruijn graphs
Language:Rust 3- Language:Shell 3
LauraSkak / Modification-count-workflow
This workflow uses Dorado, Samtools, Clair3, WhatHap and Modkit to extract a modification count table containing information for each relevant site.
Language:Python 3RhettRautsaw / VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
Language:Python 3esohkevin / ei-imputationservice
haplotype estimation, custom panel creation, and genotype imputation
Language:Nextflow 2maxibor / floria-strainer
An add-on to floria for clustering reads into strains
Language:Python 2- Language:Python 2
