https://github.com/quinlan-lab/strling

Detect novel (and reference) STR expansions from short-read data
https://github.com/quinlan-lab/strling

hacktoberfest nim-lang short-tandem-repeats str whole-genome-sequencing

Last synced: 13 days ago
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Detect novel (and reference) STR expansions from short-read data

• Host: GitHub
• URL: https://github.com/quinlan-lab/strling
• Owner: quinlan-lab
• License: mit
• Created: 2019-07-09T17:36:04.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-08-07T01:20:55.000Z (over 1 year ago)
• Last Synced: 2024-05-01T22:46:40.009Z (12 months ago)
• Topics: hacktoberfest, nim-lang, short-tandem-repeats, str, whole-genome-sequencing
• Language: Nim
• Homepage:
• Size: 416 KB
• Stars: 58
• Watchers: 7
• Forks: 9
• Open Issues: 21
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
![STRling logo](docs/strling-logo-webres.png)

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__[STRling Documentation](https://strling.readthedocs.io/en/latest/)__

STRling (pronounced like “sterling”) is a method to detect large STR expansions from short-read sequencing data. It is capable of detecting novel STR expansions, that is expansions where there is no STR in the reference genome at that position (or a different repeat unit from what is in the reference). It can also detect STR expansions that are annotated in the reference genome. STRling uses kmer counting to recover mis-mapped STR reads. It then uses soft-clipped reads to precisely discover the position of the STR expansion in the reference genome.

## Install and Run STRling

Please see the [STRling Documentation](https://strling.readthedocs.io/en/latest/) for installation and running instructions.

## Citation

For more details able the algorithm check out our paper.

If using STRling, please cite: 

Dashnow, H., Pedersen, B.S., Hiatt, L. et al. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biol 23, 257 (2022).