https://github.com/acenglish/adotto
Working space for the GIAB TR benchmarking project
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 8 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov, 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 (13.9%) to scientific vocabulary
Repository
Working space for the GIAB TR benchmarking project
Basic Info
- Host: GitHub
- Owner: ACEnglish
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Size: 44.1 MB
Statistics
- Stars: 20
- Watchers: 4
- Forks: 3
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
Project Adotto
This repo holds the analysis scripts/notes/summaries for the Genome in a Bottle Tandem Repeat Benchmark.
English, A.C., Dolzhenko, E., Ziaei Jam, H. et al. Analysis and benchmarking of small and large genomic variants across tandem repeats. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02225-z
The Benchmark
💾 Download
The current release (v1.0) of the benchmark can be found here.
📜 README
Included in the above tar-ball is a README.md which can be seen
here.
This README has details on the files contained in the benchmark as well as instructions on how to compare your
caller using Truvari. Note that Truvari is currently under active development as a part of the GIAB TR project
so a manual installation of the latest development branch is recommended. The README explains this in detail.
Other Data
The full adotto tandem-repeat catalog and pVCF of 86 haplotype-resolved assemblies created as part of this work are available via zenodo.org. Details of the files as well as download links are below.
| Dataset | Zenodo | Current Version | Details |
| ------- | ------ | --------------- | ------- |
| Catalog | 
| v1.2.1 | Link |
| Variants | 
| v0.1 | Link |
This repository
There are a few main sub-parts to this project. Each is contained in a sub-directory. Raw data that's too large to be kept on github will be made available and documented such that a user can find it and know where to place it within a clone of this repo in order to run sub-parts of the analysis.
- slides - GIAB team meeting slides
- manuscript - Summary and plotting workflows for the publication
- metadata - Data descriptor files (e.g. download paths of inputs used or sample ancestry information)
- regions - Identification of Tandem-Repeat regions of a reference
- variants - Calling variants from long-read haplotype resolved assemblies
- benchmark - Scripts for consolidating regions and variants to create the benchmark
Owner
- Name: Adam English
- Login: ACEnglish
- Kind: user
- Repositories: 7
- Profile: https://github.com/ACEnglish
GitHub Events
Total
- Issues event: 3
- Watch event: 1
- Issue comment event: 4
- Push event: 1
- Fork event: 1
Last Year
- Issues event: 3
- Watch event: 1
- Issue comment event: 4
- Push event: 1
- Fork event: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 7
- Total pull requests: 0
- Average time to close issues: about 16 hours
- Average time to close pull requests: N/A
- Total issue authors: 7
- Total pull request authors: 0
- Average comments per issue: 2.57
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: 2 days
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 3.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- CSU-KangHu (1)
- Jong-hun-Park (1)
- davidlougheed (1)
- Han-Cao (1)
- lh3 (1)
- Lionward (1)
- YaCui (1)