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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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Implementation of EukRep in the Snakemake pipeline #162

Open Rachita-Kumar opened 1 week ago

Rachita-Kumar commented 1 week ago

Hi,

I am currently trying to implement the metaGEM pipeline for the assembly and metabolic reconstruction of eukaryotic (particularly fungal) genomes. I was wondering if EukRep has been integrated into the pipeline or if there are upcoming versions that will incorporate it, since I could not locate the rule that calls this tool in the script.

Additionally, I was wondering if there are any updates or suggestions regarding the incorporation of a eukaryotic universal template for metabolic reconstruction using CarveMe. I am trying to use the reconstruction in this repository as previously suggested. However, due to the prevalent blocked reactions, I am unable to make progress in the reconstruction.

I would greatly appreciate your help and suggestions. Thank you in advance!

franciscozorrilla commented 1 week ago

Hi Rachita,

Well-spotted, indeed some of the "bonus" tools shown in the figure have not been well integrated into the current release of metaGEM, in particular when it come to the eukaryotic analysis of genomes (e.g. #159), as we chose to focus on the prokaryotic component of microbiota due to methodological limitations associated with eukaryotes. Also at one point since there were so many software dependencies for metaGEM it was impossible to conda/mamba install, so I had to cut down on non-essential dependencies. In your case I would suggest to just use EukRep as a standalone tool rather than waiting for me to impelment in metaGEM. I am definitely still interested in adding support for eukaryotic microbiome analysis (#160), I just have not found the time nor volunteers yet to address this.

There is no eukaryotic template in the original CarveMe software, however some collaborators have developed CarveFungi to generate compartmentalised models of fungal species. This might be useful for you although it is unpublished as far as I am aware. In case you have not seen them already, have a look at the repos hosted by sysbio chalmers, they develop many eukaryotic models (e.g. yeast) that could be useful for you as well.

Also just wondering, are you trying to reconstruct these eukaryotic GEMs from metagenomes? Are these from e.g. soil or from some bioreactor? Are you trying to reconstruct a specific fungal strain/species? Or just reconstruct as many GEMs as possible from a given community? If you are focused on one particular species then maybe you could do some semi-automated reconstruction from homology using RAVEN, e.g. as described in this publication.

Best, Francisco

Rachita-Kumar commented 1 week ago

Hi Francisco,

Thank you for your prompt response. Sure, I will try implementing EukRep as a standalone tool. Thank you for sharing the links to the resources, I will look into them in detail. We are indeed trying to reconstruct eukaryotic GEMs from metagenomes from different environments and were very interested in using metaGEM for the process.

Best, Rachita

franciscozorrilla commented 1 week ago

Ok, in that case I would recommend to use metaGEM (or your preferred tools) for processing metagenomes, then EukRep to separate eukaryotic contigs + EukCC to identify medium and high quality assemblies for downstream GEM reconsrtuction. Then CarveFungi to create models, which you could also analyze with SMETANA alongside your bacterial MAG-based GEMs to study interkingdom nutritional dependencies in your microbiomes of interest. Happy to help with any questions that come up along the way.

Best, Francisco

Rachita-Kumar commented 6 days ago

Hi Francisco,

Thank you very much for your suggestions, they are really helpful. I will try it out and will get back to you if I have any further questions on using metaGEM.

Best, Rachita