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NGLess Benchmarking

This repository includes code for benchmarking ngless.

Result

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

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