This repository is designed to be launched as a GitHub Codespace which serves as a demonstration environment for PacBio's Tandem Repeat Genotyper (TRGT) software.
TRGT takes advantage of PacBio HiFi reads, which are long, accurate, and include 5mC methylation calls at all CpG sites by default. It gentoypes user-specified tandem repeat locations in mapped HiFi reads and outputs its findings in standard formats. The results can also be visualised.
The whole TRGT workflow is demonstrated: raw HiFi reads are mapped against the GRCh38 chromosome 19 assembly, analysed with TRGT, then visualised.
The codespace includes the following software installed via micromamba:
To instantiate your own codespace using this repository, you'll need to be signed in to a GitHub account:
- Go to codespaces in GitHub and select 'New Codespace'
- In the 'select a repository' dropdown search for the name of this repository -
sholt6/trgt-tutorial - You may like to change Machine Type from 2-core to 4-core
- Click 'Create Codespace'
Note that the codespace will take a few minutes to set up, and will be automatically deleted after a few days of inactivity.
Instructions for the workshop itself will be provided separately.