ProGenNo/ProHap

Proteogenomics database-generation tool for protein haplotypes and variants

Language: Python - Size: 8.7 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 5 - Forks: 2

HKU-BAL/ClairS

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

Language: Python - Size: 3.46 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 51 - Forks: 5

AstraBert/AmpliPiper-docs Fork of just-the-docs/just-the-docs

Docs for AmpliPiper, developed by @nhmvienna

Language: SCSS - Size: 8.36 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

kelly-sovacool/tiger_salamander_project 📦

SNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project.

Language: Python - Size: 96.7 MB - Last synced: 8 days ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

zjwinn/HAPLOCATCHER-AN-R-PACKAGE-FOR-PREDICTION-OF-HAPLOTYPES

A data and code repository for the paper of the same name.

Size: 6.62 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

rwk-unil/sapphire

Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)

Language: C++ - Size: 7.17 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 8 - Forks: 1

ljacquin/khamix

Kernelized HAplotype-based MIXed model association mapping (KHAMIX)

Language: R - Size: 10.9 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 3 - Forks: 0

luntergroup/octopus

Bayesian haplotype-based mutation calling

Language: C++ - Size: 137 MB - Last synced: about 12 hours ago - Pushed: 9 months ago - Stars: 296 - Forks: 37

AlgoLab/Wild-pBWT Fork of msgr0/Wild-pBWT

PBWT-based algorithm for identifying all Maximal Perfect Haplotype Blocks with Wildcards

Language: C++ - Size: 50.8 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

XuewenWangUGA/VarSeqStitcher

A novel bioinformatics tool in Java to build phased long alleles of STR+SNP+InDel from VCF file

Language: HTML - Size: 91.7 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

cbg-ethz/haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

Language: C++ - Size: 1.79 MB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 24 - Forks: 35

inzilico/phase-01

Scripts to automate the phasing with several tools

Language: Python - Size: 16.6 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

PlantandFoodResearch/MCHap

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

Language: Python - Size: 15.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 17 - Forks: 3

tbrunetti/genoFinder

Haplo- and Diplotype Star Allele matcher for Drug Dosage Guidelines

Language: Python - Size: 3.34 MB - Last synced: 5 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

tsnorri/vcf2multialign

Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.

Language: C++ - Size: 1.12 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

LankyCyril/edgecase

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Language: Python - Size: 167 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 14 - Forks: 2

Cristianetaniguti/Reads2Map

WDL workflows to build genetic maps from sequencing reads

Language: WDL - Size: 167 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 6 - Forks: 0

luntergroup/bamsplit

Split a BAM file by haplotype support

Language: Python - Size: 43.9 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 15 - Forks: 1

everestial/PhaseIT

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

Language: TeX - Size: 165 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

dancooke/starfish

Intersect multiple VCF files with haplotype awareness

Language: Python - Size: 518 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 21 - Forks: 2

andrea-tango/GenHap

A Novel Computational Method Based on Genetic Algorithms for Haplotype Assembly

Language: C++ - Size: 125 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 3 - Forks: 1

vtsyvina/CliqueSNV

Language: Java - Size: 70 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 20 - Forks: 5

everestial/phase-extender

A python program that uses ReadBack phased haplotypes in population of samples and returns extended haplotype blocks.

Language: Jupyter Notebook - Size: 7.21 MB - Last synced: 6 days ago - Pushed: 7 months ago - Stars: 13 - Forks: 4

wletsou/ChromosomeOverlap

Chromosome Overlap: code accompanying "Refining the genetic risk of breast cancer with rare haplotypes and pattern-mining" by Letsou et al. DOI: 10.26508/lsa.202302183

Language: Shell - Size: 532 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

CNuge/phase-imputation

This program leverages zero recombination clusters and their relative positions on a linkage group to impute phases for missing data with high fidelity.

Language: Python - Size: 25.4 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

transbioZI/Gimpute

An efficient genetic data imputation pipeline

Language: R - Size: 2.93 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 10 - Forks: 4

zhuochenbioinfo/VCF2HAP

Construct gene haplotype with VCF format files and snpEff annotation.

Language: Perl - Size: 31.3 KB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 3

everestial/TestSwitchErrors

This is a tutorial that shows how phaseExtender can be used for recursive improvement of haplotype phasing and how to test the phasing quality by measuring switcherrors.

Language: Jupyter Notebook - Size: 185 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

everestial/phase-stitcher

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

Language: Jupyter Notebook - Size: 337 KB - Last synced: 7 days ago - Pushed: about 2 years ago - Stars: 6 - Forks: 3

everestial/VCF-Simplify

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

Language: Python - Size: 19.9 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 43 - Forks: 12

SamStudio8/gretel

An algorithm for recovering haplotypes from metagenomes

Language: Python - Size: 780 KB - Last synced: 5 days ago - Pushed: almost 3 years ago - Stars: 31 - Forks: 4

PacificBiosciences/minorseq 📦

Minor Variant Calling and Phasing Tools

Size: 1.96 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 15 - Forks: 6

edgardomortiz/fineRADstructure-tools

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

Language: Python - Size: 19.5 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 8 - Forks: 2

zhuochenbioinfo/HFI

Haplotype Fixation Index for crop populations with homozygous nature, such as rice

Language: Perl - Size: 62.5 KB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

RichardAGoldstein/HaROLD

Haplotype RecOnstruction using Longitudinal sequencing Data

Language: Java - Size: 19.7 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 3 - Forks: 1

ShujiaHuang/RefHap

A Reliable and Fast Algorithm for Single Individual Haplotyping

Language: Java - Size: 353 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 4 - Forks: 0

YaoLi3/nanopore-methylation

Long sequencing reads classifier

Language: Python - Size: 41.7 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 6 - Forks: 4

gabrielkg/croissant

Fast and simple haplotype counting.

Language: Scala - Size: 46.9 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

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: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

tsnorri/vcfdistances

Calculate SMD and Hamming and Jaccard distances between each pair of samples in a set of variant files.

Language: C++ - Size: 45.9 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

styvon/HapRecstr

a C++ program for haplotype reconstruction using HMM

Language: HTML - Size: 73.2 KB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 1