AMON on Helix
AMON (Annotation of Metabolite Origins via Networks) is an open-source bioinformatics application
that can be used to
(1) annotate which compounds in the metabolome could have been produced by bacteria present or the host;
(2) evaluate the pathway enrichment of host verses microbial metabolites, and
(3) to visualize which compounds may have been produced by host versus microbial enzymes in KEGG pathway maps.
References:
- M. Shaffer, K. Thurimella, K. Quinn, K. Doenges, X. Zhang, S. Bokatzian, N. Reisdorph and C. A. Lozupone
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
BMC Bioinformatics 2019, 20: 614. https://doi.org/10.1186/s12859-019-3176-8
Documentation
Important Notes
- Module Name: AMON (see the modules page for more information)
Interactive job
This application can only be run on Helix, and not on Biowulf.
[user@biowulf]$ ssh Helix [user@helix]$ APPS=/usr/local/apps [user@helix]$ export PATH=$APPS/AMON/1.0.0/bin:$PATH [user@helix]$ export LD_LIBRARY_PATH=$APPS/AMON/1.0.0/lib:$LD_LIBRARY_PATH [user@helix]$ export PYTHONPATH=$APPS/AMON/1.0.0/lib/pythin3.6/site-packages:$PYTHONPATH [user@helix]$ export AMON_DATA=$APPS/AMON/1.0.0/sample_dataCopy sample data to the current folder:
[user@helix]$ cp $AMON_DATA/* .Run the AMON application on the sample data:
[user@helix]$ amon.py -i ko_list.txt -o testReview the results stored in the output folder test:
[user@helix]$ ls test AMON_log.txt gene_set_1_compound_pathway_enrichment.tsv origin_table.tsv enrichment_heatmap.png kegg_mapper.tsv [user@helix]$ head test/kegg_mapper.tsv 0 C02631 blue K13489 blue C03287 blue K00926 blue C20423 blue K08224 blue K00800 blue K00162 blue K01505 blue [user@helix]$ head -n 10 test/gene_set_1_compound_pathway_enrichment.tsv pathway size overlap probability adjusted probability Purine metabolism 95 70 1.5357411062115152e-24 3.2404137341062968e-22 Methane metabolism 86 63 4.696075577134766e-22 4.954359733877178e-20 Aminoacyl-tRNA biosynthesis 52 44 1.0032329802784207e-20 7.05607196129156e-19 Folate biosynthesis 57 45 1.1333844794425998e-18 5.978603129059714e-17 Pentose phosphate pathway 35 32 3.680767932496869e-18 1.5532840675136786e-16 Lipopolysaccharide biosynthesis 54 42 4.0149350164351284e-17 1.4119188141130203e-15 Glycolysis / Gluconeogenesis 31 28 7.816512870575171e-16 2.3561203081305158e-14 Central carbon metabolism in cancer 37 31 4.8353494377765e-15 1.2753234142135519e-13 Phosphotransferase system (PTS) 57 41 1.266083970361715e-14 2.968263530514687e-13Visualize the output heat map:
[user@helix]$ show_image.py test/enrichment_heatmap.png

End the interactive session:
[user@helix ~]$ exit [user@biowulf ~]$