hj1994412 / emapper-benchmark

Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.

Scripts and global analysis of eggNOG-mapper performance compared against BLAST, InterProScan and CAFA2. Genomes and metagenomes evaluated.

Supplementary Material for the paper: "Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper" http://biorxiv.org/content/early/2016/09/22/076331

Analysis

Additional figures and details are available as jupyter notebook in this reposotory.

Reproducibility

Benchmark required running BLAST, InterProScan and eggNOG-mapper independently and, in the case of eggNOG-mapper, using multiple combinations of parameters.

All raw data (~55GB uncompressed) can be downloaded from: http://beta-eggnogdb.embl.de/download/eggnog_4.5/eggnog-mapper-data/emapper_benchmark_data.tar.gz

Data includes 4 self-explanatory directories:

  blast/
  interpro/
  emapper_hmm/
  emapper_diamond/

To re-run the whole benchmark analysis, decompress all 4 directories under within this repository, and execute benchmark.py, which will generate a digested all_benchmark_tables.pkl file to be used within the jupyter notebook.