esohkevin/ei-imputationservice

haplotype estimation, custom panel creation, and genotype imputation

Language: Nextflow - Size: 256 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 2 - Forks: 0

esohkevin/ei-gwas

gwas workflow from raw intensity data to in-silico functional mapping

Language: Shell - Size: 15.5 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 3 - Forks: 0

nf-core/phaseimpute

A bioinformatics pipeline to phase and impute genetic data

Language: Nextflow - Size: 17 MB - Last synced at: about 9 hours ago - Pushed at: about 9 hours ago - Stars: 22 - Forks: 20

wangyibin/CPhasing

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

Language: Python - Size: 70.5 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 37 - Forks: 4

Plant-Food-Research-Open/assemblyqc

A Nextflow pipeline for evaluating assembly quality

Language: Nextflow - Size: 64.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 34 - Forks: 7

HKU-BAL/ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

Language: Python - Size: 12.7 MB - Last synced at: 24 days ago - Pushed at: 25 days ago - Stars: 84 - Forks: 8

zengxiaofei/HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

Language: Python - Size: 42 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 192 - Forks: 8

MeHelmy/princess

Language: Python - Size: 1.51 MB - Last synced at: 8 days ago - Pushed at: 4 months ago - Stars: 80 - Forks: 8

zhangrengang/subgenome_phasing_example

An Example of Subgenome Phasing for Complex Allopolyploidy

Language: Python - Size: 147 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 1

atgu/GWASpy

GWAS QC, PCA, haplotype phasing, genotype imputation

Language: Python - Size: 6.31 MB - Last synced at: 29 days ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 5

luntergroup/octopus

Bayesian haplotype-based mutation calling

Language: C++ - Size: 138 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 312 - Forks: 37

fedarko/strainFlye

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

Language: Python - Size: 14.4 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 11 - Forks: 2

PacificBiosciences/HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads

Language: Rust - Size: 796 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 72 - Forks: 4

zhangrengang/SubPhaser

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

Language: Python - Size: 3.26 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 58 - Forks: 12

AI-sandbox/aegen

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

Language: Python - Size: 19.2 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 2

OmarOakheart/nPhase

Ploidy agnostic phasing pipeline and algorithm

Language: Python - Size: 50.5 MB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 45 - Forks: 5

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.

Language: R - Size: 625 KB - Last synced at: 24 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 3

DEploid-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++ - Size: 156 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 20 - Forks: 10

odelaneau/shapeit5

Segmented HAPlotype Estimation and Imputation Tool

Language: C++ - Size: 1.22 GB - Last synced at: 5 months ago - Pushed at: 11 months ago - Stars: 73 - Forks: 12

everestial/VCF-Simplify

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

Language: Python - Size: 19.9 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 47 - Forks: 11

maxibor/floria-strainer

An add-on to floria for clustering reads into strains

Language: Python - Size: 7.03 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

stjude/indelPost

Python library for simple and complex indels.

Language: C - Size: 1.17 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 3

manuelgug/FapR

Frequency-based amplicon phasing in R

Language: R - Size: 2.68 MB - Last synced at: 10 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

PacificBiosciences/minorseq 📦

Minor Variant Calling and Phasing Tools

Size: 1.96 MB - Last synced at: 12 months ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 6

selfdecode/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 - Size: 23.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 3

plantformatics/phaseLD

LD-based phasing algorithm for segregating F1 populations (pseudo-oneway testcross)

Language: Perl - Size: 5.55 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

inzilico/phase-01

Scripts to automate the phasing with several tools

Language: Python - Size: 16.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

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 - Size: 225 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

victimofleisure/TripLight

psychedelic visual synthesizer color-organ style

Language: C++ - Size: 280 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

srubinacci/imputation-ukb-ref-panel

Genotype imputation pipelines for the UK Biobank Research Analysis Platform

Language: Shell - Size: 34.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 0

MaddalenaCella/lcWGS_EquCab

Language: R - Size: 745 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

everestial/PhaseIT

A pipeline for phasing haploptypes using short readbackphased haplotype blocks in population of samples.

Language: TeX - Size: 165 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

PengJia6/MSHunter 📦

Microsatellite genotyping

Language: Python - Size: 114 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

inzilico/kselection

A pipeline to select the best K (number of clusters) for fastPHASE imputation and phasing.

Language: R - Size: 11.7 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

dzhigaevd/phasor

Easy, fast, configurable version of phasor. Perfect for students who what to start with analyzing Coherent X-ray Diffraction Data.

Language: MATLAB - Size: 7.03 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

acostauribe/TANGL

Set of scripts used for the paper "A Neurodegenerative Disease Landscape of Rare Mutations in Colombia Due to Founder Effects"

Language: Shell - Size: 1.96 MB - Last synced at: 7 months ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 3

transbioZI/Gimpute

An efficient genetic data imputation pipeline

Language: R - Size: 2.93 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 4

CERC-Genomic-Medicine/shapeit4_pipeline

Pipeline for genotype phasing using SHAPEIT4

Language: Nextflow - Size: 6.84 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

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 - Size: 10.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 3

everestial/phase-stitcher

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

Language: Jupyter Notebook - Size: 337 KB - Last synced at: 11 months ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 3

sonisarm/Comparing-phasing-outputs

Step-by-step guide to different types of phasing and testing their accuracy

Language: R - Size: 5.61 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

BIGCS-Lab/phimtools

A phasing and imputation pipeline for NGS data

Language: Python - Size: 41.9 MB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 1

koesterlab/microphaser

Language: Rust - Size: 1.91 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 2

bpucker/yam

scripts associated with yam genome assembly

Language: Python - Size: 69.3 KB - Last synced at: 11 months ago - Pushed at: about 5 years ago - Stars: 7 - Forks: 0

RhettRautsaw/VariantCaller

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

Language: Python - Size: 22.5 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

cnettel/jackdaw

Tools for handling phase retrieval and related tasks in sparse (low-signal) X-ray single particle imaging applications, specifically COACS.

Language: Jupyter Notebook - Size: 2.39 MB - Last synced at: 8 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

everestial/SmallTools

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

Language: Python - Size: 3.61 MB - Last synced at: over 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0