Additional tutorials

To use microbetag there are two main approaches:

  • with microbetagDB through Cytoscape; in this case, your taxa will be mapped to a GTDB representative genome if possible and pre-calculations will be used for the annotation step. However, if you have an abundance table with more than 1000 sequences, you will have to provide a network. To enable this and at the same time to support the taxonomy annotation of 16S rRNA sequences directly with GTDB, if that is your case, we provide a containerized image, called microbetag_prep, for what the preparation step. This is only required if you have more than 1000 sequences and your taxonomy is neither Silva nor GTDB.
  • applying the microbetag workflow to your own bin/MAGs locally and then visualize the annotated network through Cytoscape; in this case, you will use another Docker/Singularity image we provide to annotate your genomes locally. This, based on the number of genomes/MAGs you have, may take several hours and thus, cannot be performed on-the-fly as a web-service, so you will have to run it locally. Once you get the annotated network, then you can use the CytoscapeApp we provide to visualize it.

The simplest case is you are about to use the first approach where your sequences are less than 1000 (up limit for the server to build a network). In this case, you may follow directly the instructions described in the Cytoscape tutorials. If you have a more complex data set, then you need to:

  • either perform the microbetag_prep step, where you get a network again using FlashWeave and/or a GTDB-based taxonomy assignment of your amplicon sequences (if that is your case), or
  • perform microbetag locally, in case you have your own genomes to use instead of the GTDB representative ones

Here, we provide three tutorials:

For any issues, bugs, questions, feel free to contact us on Matrix or just open an issue on our GitHub repo.

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