https://github.com/midnighter/kraken2-bracken-test-db
Temporary place to host the kraken2 & Bracken database construction pipeline.
https://github.com/midnighter/kraken2-bracken-test-db
Last synced: 3 months ago
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Temporary place to host the kraken2 & Bracken database construction pipeline.
- Host: GitHub
- URL: https://github.com/midnighter/kraken2-bracken-test-db
- Owner: Midnighter
- License: mit
- Created: 2022-10-12T08:07:30.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-10-12T08:07:54.000Z (over 3 years ago)
- Last Synced: 2025-02-23T09:30:29.949Z (over 1 year ago)
- Language: Nextflow
- Size: 3.71 MB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Build kraken2 & Bracken test database
Use the test genomes to create a
[kraken2](https://github.com/DerrickWood/kraken2) database and
[bracken](https://github.com/jenniferlu717/Bracken) classifier mappings for
different expected read lengths.
## Usage
1. Set up nextflow as [described
here](https://www.nextflow.io/index.html#GetStarted).
2. If you didn't run this pipeline in a while, possibly update nextflow itself.
```
nextflow self-update
```
3. Then run the pipeline.
```
nextflow -c anton.config run main.nf -profile docker
```
## Copyright
- Copyright © 2022, Moritz E. Beber.
- Free software, distributed under the [MIT license](LICENSE)