Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: RafPrograms
- License: gpl-3.0
- Language: C++
- Default Branch: main
- Size: 917 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
HaploGI – Haplotyping Given Inheritance
Pedigree-Based Haplotyping\ Version 1.0.0
Author
Rafael A. Nafikov\ Division of Medical Genetics, Department of Medicine\ University of Washington
Last modified on: June 28, 2025
Contents
- Introduction
- Paper Citation
- Software Citation
- License
- Software URL
- Data Example
- HaploGI Utility Scripts
- Support
Introduction
HaploGI (Haplotyping Given Inheritance) performs pedigree-based haplotyping of Whole Genome Sequencing (WGS) data and determines haplotype sharing between subjects from a specified group of cases.
Paper Citation
If you use HaploGI in your work, please cite:
Nafikov, R. A., Sohi, H., Nato Jr, A. Q., Horimoto, A. R., Bird, T. D., DeStefano, A., Blue, E. E., & Wijsman, E. M.\ Variant prioritization by pedigree-based haplotyping. Submitted for publication to Genetic Epidemiology, 2025.
Software Citation
If you use HaploGI in your research, please also cite the following:
📦 Software
bibtex
@software{nafikov_2025_haplogi,
author = {Rafael A. Nafikov},
title = {HaploGI - Haplotyping Given Inheritance},
version = {1.0.0},
year = 2025,
publisher = {Zenodo},
doi = {10.5281/zenodo.15860913},
url = {https://doi.org/10.5281/zenodo.15860913}
}
This repository includes a CITATION.cff file. On GitHub, you can click the “Cite this repository” button near the top of the page to view citation information in multiple formats (BibTeX, EndNote, RIS, etc.).
License
HaploGI is a C++ program released under the GNU General Public License v3.0.\ See LICENSE for full terms.
© 2025 Rafael A. Nafikov
Software URL
HaploGI source code is available at:\ 👉 https://github.com/RafPrograms/HaploGI/tree/main/src
HaploGI documentation and a parameter file template to run the program are available at:\ 👉 https://github.com/RafPrograms/HaploGI/tree/main/docs
Data Example
Downloadable ZIP with example input/output for each run option is available at:\ 👉 https://github.com/RafPrograms/HaploGI/tree/main/data_example
HaploGI Utility Scripts
A number of Python utility scripts are available to assist with preparing HaploGI input files, processing output data, and visualizing results, at:\ 👉 https://github.com/RafPrograms/HaploGI/tree/main/HaploGI_utility_scripts
Support
For questions, bug reports, or suggestions, please contact:\ 📧 nrafscience\@gmail.com\ 🔗 GitHub Issues
Owner
- Name: Rafael Nafikov
- Login: RafPrograms
- Kind: user
- Repositories: 1
- Profile: https://github.com/RafPrograms
Citation (CITATION.cff)
cff-version: 1.2.0
message: >
If you use this software, please cite it using the metadata below.
Also consider citing our paper, listed in the README.
type: software
title: "HaploGI - Haplotyping Given Inheritance"
version: "1.0.0"
doi: 10.5281/zenodo.15860913
date-released: 2025-07-08
authors:
- family-names: Nafikov
given-names: Rafael A.
orcid: https://orcid.org/0000-0001-7288-0981
license: GPL-3.0-only
repository-code: https://github.com/RafPrograms/HaploGI
url: https://github.com/RafPrograms/HaploGI
abstract: >
HaploGI (Haplotyping Given Inheritance) is a software package developed for
pedigree-based haplotyping of whole-genome sequencing (WGS) data and determination
of haplotype sharing between subjects. It aims to identify risk haplotypes within
linkage regions and disease-associated variants carried on those haplotypes.
This version (v1.0.0) is associated with our 2025 presubmission to the journal
Genetic Epidemiology (Nafikov et al., 2025).
GitHub Events
Total
- Release event: 1
- Push event: 3
- Public event: 1
- Create event: 1
Last Year
- Release event: 1
- Push event: 3
- Public event: 1
- Create event: 1