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https://github.com/broadinstitute/str-truth-set

Genome-wide tandem repeat (TR) truth set based on the Synthetic Diploid Benchmark [Li et al. 2018]

https://github.com/broadinstitute/str-truth-set

Science Score: 57.0%

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    Found .zenodo.json file
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    Found 1 DOI reference(s) in README
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    Links to: biorxiv.org, ncbi.nlm.nih.gov
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    Organization broadinstitute has institutional domain (www.broadinstitute.org)
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    Low similarity (4.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Genome-wide tandem repeat (TR) truth set based on the Synthetic Diploid Benchmark [Li et al. 2018]

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 14 MB
Statistics
  • Stars: 8
  • Watchers: 2
  • Forks: 0
  • Open Issues: 1
  • Releases: 1
Created over 3 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

Code for creating and analyzing a genome-wide tandem repeat (TR) truth set based on publicly-available data from the Synthetic Diploid Benchmark [Li et al. 2018]

For more details, see:

Insights from a genome-wide truth set of tandem repeat variation Ben Weisburd, Grace Tiao, Heidi L. Rehm bioRxiv 2023.05.05.539588

Creating the truth set

After cloning this repo, see: ./run_all_steps.sh This script runs all the steps for creating the truth set, launching downstream analyses, and generating the tables & figures for the paper.

Tool comparisons

Results from benchmarking widely-used STR callers using this truth set:

https://broadinstitute.github.io/str-truth-set/html/toolcomparisonviewer.html

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

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Top Authors
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  • HLHsieh (1)
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  • bw2 (1)
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