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Read-only view of a live SciFlow workflow — this is the actual pipeline that produced these results, not a mockup. Shotgun Metagenomics — Human Gut Microbiome Profile (SciFlow). Open any stage to inspect its parameters, command, versions, inputs and outputs.
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May 30, 2026
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metagenomics microbiome shotgun taxonomic-profiling gut kraken2
Created May 30, 2026 at 20:01
Which species dominate a real human gut metagenome? This demo profiles DRR232287 — a modern Illumina 2×150 PE paired-end stool sample from a healthy donor — through QC, Kraken2 classification against the full standard database, and Bracken species-level re-estimation. Key results from this run: 89.58% of reads classified. Top species: Phocaeicola vulgatus 31.4%, Bacteroides stercoris 14.2%, Bifidobacterium breve 9.9%, Bifidobacterium pseudocatenulatum, Escherichia coli. A textbook Bacteroidota-dominant healthy gut profile with a strong Bifidobacterium component — consistent with a Westernised adult microbiome. Pipeline: fastp read QC → Kraken2 k-mer LCA classification (full standard DB, bacteria + archaea + viral + human) → Bracken 2.9 species-level abundance re-estimation → taxonomic summary. Built for microbiome and clinical-metagenomics groups who want a reproducible, high-sensitivity read-based profiling workflow on genuinely public data without assembling five tools by hand.