https://github.com/applicativesystem/pacbiohifi-report-classifier
pacbiohifi report classifier for any sequencing startups
https://github.com/applicativesystem/pacbiohifi-report-classifier
bioinformatics genome-analysis pacbio-data pacbio-sequencing pacbiohifi python3
Last synced: 6 months ago
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pacbiohifi report classifier for any sequencing startups
- Host: GitHub
- URL: https://github.com/applicativesystem/pacbiohifi-report-classifier
- Owner: applicativesystem
- License: mit
- Created: 2024-08-17T19:24:00.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-08-17T19:25:18.000Z (10 months ago)
- Last Synced: 2024-11-10T20:18:14.801Z (8 months ago)
- Topics: bioinformatics, genome-analysis, pacbio-data, pacbio-sequencing, pacbiohifi, python3
- Language: Python
- Homepage:
- Size: 27.3 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# pacbiohifi-seq-app
- a single page shiny express pacbiohifi-seq-app for profiling of the pacbiohifi sequencing reads sequencing facility or startups.
- shiny API reference is located at [python API](https://shiny.posit.co/py/api/) and also here [express API](https://shiny.posit.co/py/docs/express-in-depth.html)
- You can also host on tapyr template [template](https://github.com/Appsilon/tapyr-template)
- parameters to set: fastq file path, readfiltercutoff, provide the name and the address of the sequencing facility, provide the name and the person responsible for sequencing.
- installation dependencies
```
# First install htmltools, then shiny
pip install https://github.com/posit-dev/py-htmltools/tarball/main
pip install https://github.com/posit-dev/py-shiny/tarball/main
pip install shiny
pip install shinywidgets
pip install shinylive
pip install shinyswatch
```
- to use and build a dashboard will be build for the complete analysis including the name of the sequencing facility or center and the person
```
git clone https://github.com/gauravcodepro/pacbiohifi-seq-app.git
cd pacbiohifi-seq-app
# put the fastq reads files there. provide the parameters and run as
shiny run pacbiohifi-seq-app.py app.py --reload
```
- **To do today: bin according to the struger rule, bug check**
Gaurav Sablok