FAQs

Why did you develop metaGEM?

We developed metaGEM as a workflow to generate and simulate community level metabolic exchanges between prokaryotic genome scale metabolic models directly from metagenomic data.

Why the name metaGEM?

It named after the concept of metagenome-based genome scale metabolic models. It also sounds better than the previous name: metaBAGpipes 👎

What data files does metaGEM take as input?

The metaGEM workflow was designed to work with raw short read sequencing data.

Can metaGEM handle single-end read datasets?

Ideally you have paired end reads, but we also provide a modified Snakefile for working with single end read datasets.

Does metaGEM support long reads?

Although it is on the horizon, metaGEM does not currently support long reads or hybrid assembly methods.

Do I need to start from raw sequences?

No, you can also use metaGEM to bin your pre-assembled contigs or to generate metabolic models for your pre-binned MAGs (metagenome assembled-genomes).

Do I need access to a high performance computer cluster?

Depends on what data you are working with. For example, if you are starting from raw short reads then you will not be able to assemble them with the computational resources present in most personal computers, and you will likely need access to your institution's HPCC. However, if you are starting from pre-binned MAGs then you should have no problem generating metabolic models on your personal computer.