hariszaf/microbetag_prep repository overview

This image enables users to preprocess an abundance table the best way possible for using microbetag⁠

It supports 2 main processes:

• taxonomy assignment of 16S rRNA OTUs/ASVs to GTDB taxonomies thanks to the DADA2 formatted⁠ extraction of the related sequences and the IDTAXA⁠ algorithm of the DECIPHER toolset.
• building of a co-occurrence network with FlashWeave⁠

The first module is essential for getting the most relevant annotations microbetag can get but also, makes microbetag much more time efficient as it does not need to map non standard taxonomy schemes to the taxonomies supported on microbetagDB.

The second module is essential for the network itself as it allows the user to tune the FlashWeave parameters the best way for them.

In all cases, performing this pre-processing is mandatory when the abundance table consists of more than 1,000 taxa.

For more information on how to run this image, please check here⁠.

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microbetag on GitHub:

• bringing the pieces together⁠
• the app⁠
• the GUI⁠

In the same DockerHub repo, we also keep the microbetag_prep:base, which works as the base image to build upon our code (Dockerfile.base⁠). This image is not supposed to change in time. Any updates on the dependencies needed or any new ones will be directly added on the Dockerfile of the the microbetag_prep image (Dockerfile⁠)