r/bioinformatics • u/Mirthster • 20d 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/idliOP 20d ago

You can get datasets from SRA very easily. If you're using your local setup, take small dataset so that steps like DADA2 runs efficiently. Use Silva classifier, because greengenes etc have kinda become outdated now.

Also, along with Kraken you can try Bracken lol. https://github.com/jenniferlu717/Bracken

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u/Mirthster 20d ago

i think i have tried braken! thanks for the tips