hiphase
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
Science Score: 44.0%
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
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Keywords
Repository
Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
Basic Info
Statistics
- Stars: 72
- Watchers: 7
- Forks: 4
- Open Issues: 2
- Releases: 20
Topics
Metadata Files
README.md
HiPhase
A tool for jointly phasing small, structural, and tandem repeat variants for PacBio sequencing data
HiPhase will phase variant calls made from PacBio HiFi datasets. Key features relative to other phasing tools include:
- Joint phasing of small variants and structural variants
- Support for multi-allelic variation
- Creates longer, correct phase blocks relative to the current best practice
- No downsampling of the data
- Novel algorithms: dual-mode allele assignment and core A* phasing algorithm
- Quality of life additions: innate multi-threading, simultaneous haplotagging and statistics generation
Authors: Matt Holt, Chris Saunders
Availability
Documentation
Citation
If you use HiPhase, please cite our publication:
Original BioRxiv pre-print:
Need help?
If you notice any missing features, bugs, or need assistance with analyzing the output of HiPhase, please don't hesitate to open a GitHub issue.
Support information
HiPhase is a pre-release software intended for research use only and not for use in diagnostic procedures. While efforts have been made to ensure that HiPhase lives up to the quality that PacBio strives for, we make no warranty regarding this software.
As HiPhase is not covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any HiPhase release. Please report all issues through GitHub instead. We make no warranty that any such issue will be addressed, to any extent or within any time frame.
DISCLAIMER
THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.
Owner
- Name: PacBio
- Login: PacificBiosciences
- Kind: organization
- Email: github@pacb.com
- Location: Start from the website below!
- Website: http://pacb.com
- Twitter: pacbio
- Repositories: 50
- Profile: https://github.com/PacificBiosciences
Citation (CITATION.bib)
@article{holt2024hiphase,
title={HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing},
author={Holt, James M and Saunders, Christopher T and Rowell, William J and Kronenberg, Zev and Wenger, Aaron M and Eberle, Michael},
journal={Bioinformatics},
pages={btae042},
year={2024},
publisher={Oxford University Press}
}
GitHub Events
Total
- Create event: 2
- Release event: 1
- Issues event: 25
- Watch event: 8
- Delete event: 1
- Issue comment event: 63
- Push event: 3
- Pull request review event: 1
- Pull request event: 2
Last Year
- Create event: 2
- Release event: 1
- Issues event: 25
- Watch event: 8
- Delete event: 1
- Issue comment event: 63
- Push event: 3
- Pull request review event: 1
- Pull request event: 2
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 8
- Total pull requests: 0
- Average time to close issues: 22 days
- Average time to close pull requests: N/A
- Total issue authors: 6
- Total pull request authors: 0
- Average comments per issue: 5.38
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 0
- Average time to close issues: 22 days
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 0
- Average comments per issue: 5.38
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mrvollger (4)
- ywzhang071394 (3)
- WeiCSong (3)
- jennyp76 (2)
- davidyuyuan (2)
- hangsuUNC (2)
- Han-Cao (2)
- DayTimeMouse (1)
- ClarenceHsiang (1)
- minw2828 (1)
- andyjslee (1)
- Oracle6543 (1)
- Maille0 (1)
- charliechen912ilovbash (1)
- GuidoGallo (1)
Pull Request Authors
- holtjma (8)
- davidyuyuan (1)
- hangsuUNC (1)