https://github.com/ngless-toolkit/ngless2018benchmark
Benchmarking ngless
https://github.com/ngless-toolkit/ngless2018benchmark
benchmark benchmarking benchmarking-ngless bioinformatics next-generation-sequencing ngless
Last synced: about 2 months ago
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Benchmarking ngless
- Host: GitHub
- URL: https://github.com/ngless-toolkit/ngless2018benchmark
- Owner: ngless-toolkit
- Created: 2017-04-27T14:07:32.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2019-06-13T15:15:22.000Z (almost 6 years ago)
- Last Synced: 2025-02-12T19:40:32.644Z (3 months ago)
- Topics: benchmark, benchmarking, benchmarking-ngless, bioinformatics, next-generation-sequencing, ngless
- Language: Python
- Homepage: https://ngless.embl.de
- Size: 5.5 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# NGLess Benchmarking
This repository includes code for benchmarking [ngless](https://ngless.embl.de).
This is a companion repository to:
> _NG-meta-profiler: fast processing of metagenomes using NGLess, a
> domain-specific language_ by Luis Pedro Coelho, Renato Alves, Paulo Monteiro,
> Jaime Huerta-Cepas, Ana Teresa Freitas, and Peer Bork _in_ Microbiome 7:84 (2019)
> [http://doi.org/10.1186/s40168-019-0684-8](http://doi.org/10.1186/s40168-019-0684-8)
## Reproducing
### From scratch
1. Download all data: run the script `download-data.py`. This will download
from ENA into a directory `data/` (this process can take several hours and will
result in ca. 60GiB of data).
### Using the precomputed results
1. Precomputed data is available in `data/precomputed`
2. The script `sources/plot-comparison.py` generates the comparison plot