https://github.com/bcgsc/link_str

Analysis scripts developed for genotyping STRs in linked-read data
https://github.com/bcgsc/link_str

Last synced: 10 months ago
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Analysis scripts developed for genotyping STRs in linked-read data

• Host: GitHub
• URL: https://github.com/bcgsc/link_str
• Owner: bcgsc
• License: gpl-3.0
• Created: 2021-08-24T20:20:19.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2022-03-17T21:12:01.000Z (almost 4 years ago)
• Last Synced: 2024-07-31T20:29:00.473Z (over 1 year ago)
• Language: Python
• Size: 1.78 MB
• Stars: 1
• Watchers: 6
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-linked-reads - Link_STR - read data| (Tools)

README

          
# Genotyping STRs in linked-read data

This repository contains Python scripts developed to:

- extract in-repeat repeats (IRRs) using barcodes from linked-read alignments ([IRR extraction](irr))

- estimate sizes of genomic intervals by calculating Jaccard index (JI) of barcode sharing ([distance estimate](jaccard_index))

## Dependancies

- [NumPy](https://numpy.org/)

- [Pandas](https://pandas.pydata.org/)

- [pybedtools](https://daler.github.io/pybedtools/)

- [pysam](https://github.com/pysam-developers/pysam)

- [TRF](https://tandem.bu.edu/trf/trf.html) (for IRR extraction)

- [blastn](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) (for IRR extraction)

Author: [Readman Chiu](mailto:rchiu@bcgsc.ca)

:copyright: Canada's Michael Smith Genome Sciences Centre, BC Cancer