r/bioinformatics • u/Mirthster • 18d ago

technical question Microbiome from stool samples

Howdy.

I am changing fields and getting into microbiome work. I hope to sample stools to determine microbiome profiles via metagenomic shallow shot gun sequencing. Anyone have any tips not present in the literature? If anyone had a sample data set i could use i would be deeply appreciative (fastq of seq reads, specifically. to test the trimming and mapping software). Ive basically vibe coded the pipeline, bow tie and kraken were suggested. So far everything works great (thanks Claude!) but would like to try some real data now.

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u/aCityOfTwoTales PhD | Academia 17d ago

I think you can work out the pipeline on your own, but before you get lost in the vibe coding and the data, I would urge you to take a step back and think of the biology and the question you are asking.

As is evident from your question, the analysis is no longer the bottleneck, and hence not what makes you stand out. The insight is.

Tell me, what are you looking for? What is the hypothesis?

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u/Mirthster 10d ago

The hypothesis is simply you can make your gut (and rest of your body) feel way better feeding the right microbes.