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