hariszaf/microbetag repository overview

⁠About

microbetag is a microbial interactions co-occurrence network annotator.

It focuses on amplion data and using an OTU-table as an entry point, it builds a co-occurrence network (if there is not one already provided by the user) using FlashWeave⁠ [1].

microbetag has 2 main modules:

• the pathway complementarity module: after integrating more than 20K high quality genomes from resources such as GTDB⁠ [2], KEGG ORGANISMS⁠ [3] and the MGnify catalogues⁠ [4], microbetag focuses on the associations between species and strains and returns potential metabolic interactions between the pairs of the network

• the environmental conditions and phenotypic data module: resources such as FAPROTAX⁠ [5] and BugBase⁠ [6] are exploited to annotate each node of the co-occurrence network with labels such as metabolic processes that has been found related to, its oxidative tolerance etc.

⁠Pull and run

To get microbetag, the user needs to have Docker locally. To install Docker you may follow the instuctions here⁠.

Once Docker is available, the user needs to pull microbetag by running

docker push hariszaf/microbetag

This way, the latest version of microbetag will be downloaded. Otherwise, the user might specify which version of microbetag needs to pull by running instead:

docker push hariszaf/microbetag:tagname

for the list of versions available, you may see the Tags and Scans list.

Once microbetag has been downloaded, the user needs to fill in a config.yml file setting the parameters of his/her choice.

Then microbetag is ready to go, either by opening a docker shell first:

docker run --rm -it -v /<path_to_input_folder>/:/mnt hariszaf/microbetag
./microbetag.py -conf /mnt/confing.yml

⁠Status

Under development

GitHub repo: https://github.com/hariszaf/microbetag/⁠

⁠References

[1] Tackmann, Janko, João Frederico Matias Rodrigues, and Christian von Mering. "Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data." Cell systems 9.3 (2019): 286-296.

[2] Parks, Donovan H., et al. "A complete domain-to-species taxonomy for Bacteria and Archaea." Nature biotechnology 38.9 (2020): 1079-1086.

[3] Kanehisa, Minoru, et al. "KEGG: new perspectives on genomes, pathways, diseases and drugs." Nucleic acids research 45.D1 (2017): D353-D361.

[4] Mitchell, Alex L., et al. "MGnify: the microbiome analysis resource in 2020." Nucleic acids research 48.D1 (2020): D570-D578.

[5] Louca, Stilianos, Laura Wegener Parfrey, and Michael Doebeli. "Decoupling function and taxonomy in the global ocean microbiome." Science 353.6305 (2016): 1272-1277.

[6] Ward, Tonya, et al. "BugBase predicts organism-level microbiome phenotypes." BioRxiv (2017): 133462.