About the Metagenomics: Tools, Workflows & Questions category

Metagenomics: Tools, Workflows & Questions
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Ask questions and share ideas about metagenomics datasets, tools, workflows, results, and troubleshooting. Learn from others as you develop and test your analyses.

Use this category when you are exploring or troubleshooting a metagenomics analysis. Tell us what you are trying to find out, what dataset you are using, and what you have tried so far.

When asking for help, include enough information for others to understand your work. This might include:

  • your dataset or accession number;
  • sequencing type, if known;
  • the tool or workflow you are using;
  • a link to your Galaxy history;
  • the result, error, or output you are trying to understand;
  • what you expected to happen;
  • your specific question.

You do not need to have a successful analysis before posting. Unexpected results, failed tools, and questions about what to try next are all part of the research process.

If you have experience with a tool, dataset, or approach someone is asking about, please contribute. The goal is to build a community where we can learn metagenomics by working through real research problems together.

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Hi Dr. Guthrie! My name is Bre and I’m hoping to become a PA. I have a bachelor’s degree in kinesiology, currently work in cardiology, & recently applied to PA school.

I’m really interested in exploring how the gut microbiome connects to chronic kidney disease. I’d like to learn more about microbial metabolism and how metabolomics connects to the metagenomics work we’ve been doing. I’m also open to exploring how microbes or viruses might contribute to disease.

So far I’ve been learning Galaxy using seawater and human gut datasets. With the gut dataset, I checked read quality, randomly selected 10% of the reads, assembled them with Flye, & evaluated the assembly with QUAST. I’m getting more comfortable with the tools but I’m still learning how to interpret the results and decide what to do next.

I’m excited to work toward a focused project that connects to my interest in medicine. I’d love your guidance on what CKD related questions might be a good fit for the available data.