SciFlow lab notebook · Shared read-only

Shotgun Metagenomics — Human Gut Microbiome Profile (SciFlow)

Which species dominate a real human gut metagenome?

metagenomicsmicrobiomeshotguntaxonomic-profilinggutkraken2

Overview Methods & provenance Results Raw artifacts

Run date

2026-06-01

Stages

3 3 completed

Pipeline

metag_decon → kraken2 → taxonomic_classify

Software

staphb/kraken2:2.1.3

Outputs

22 files 331.2 MB

Overview

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.

Methods & per-stage provenance

3 stages, 3 completed. Each stage below lists the parameters it ran with, the software the run recorded, and the files it produced.

Not recorded by this run
  • no figures rendered (no PNG/SVG outputs and no Plotly HTML figure could be extracted)
01 Host QC + Decontamination (fastp + bowtie2-GRCh38) metag_decon 1.0 h completed

fastp adapter/quality trim of the raw shotgun reads before profiling.

forward reads: DRR232287_sub1M_R1.fastq.gzreverse reads: DRR232287_sub1M_R2.fastq.gzhost index prefix: /databases/grch38_bt2/GCA_000001405.15_no_alt_plus_hs38d1/GRCh38_noalt_decoy_asmin length: 50min quality: 20skip decon: off

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata
  • bowtie2.loglog · 604 B
  • fastp.htmlreport · 473 KB
  • fastp.jsondata · 128 KB
  • fastp.loglog · 2 KB
  • host_flagstat.txttext · 492 B
  • host_removed_R1.fastq.gzGZ · 72.2 MB
  • host_removed_R2.fastq.gzGZ · 74.0 MB
  • input_data_summary.htmlreport · 1.7 MB
  • multiqc.loglog · 455 B
  • multiqc_report.htmlreport · 2.1 MB
  • summary.jsondata · 446 B
  • trimmed_R1.fastq.gzGZ · 21.2 MB
  • trimmed_R2.fastq.gzGZ · 22.2 MB
  • unpaired_R1.fastq.gzGZ · 705 KB
  • unpaired_R2.fastq.gzGZ · 1.0 MB
02 Kraken2 Taxonomic Classification kraken2 1.0 h completed

Which species are in this microbiome sample? Kraken2 k-mer LCA classification against the standard-8gb DB (bacteria + archaea + viral + human). Produces kraken2_report.txt + per-read output.

forward reads: host_removed_R1.fastq.gzreverse reads: host_removed_R2.fastq.gzdatabase: /databases/kraken2/k2_standard_20240605confidence: 0.1min hit groups: 2target genus:

Verbatim command / script not recorded in this run's stage record.

Container image: staphb/kraken2:2.1.3 Image digest: sha256:53aee35987059ae177301e6bdeceb1524a4bcf7b0eb0ef0842d8578b6bf1a5ee
  • kraken2.loglog · 200 B
  • kraken2_output.txttext · 135.5 MB
  • kraken2_report.txttext · 50 KB
  • summary.jsondata · 2 KB
03 Species Answer (parse Kraken2 report) taxonomic_classify 1.0 h completed

Parses the Kraken2 report into a normalized species-level answer with confidence — the user-facing 'who is in this sample?' summary.

engine: bacteriamode: from_kraken_reportread length: 150confidence threshold: 0.1kraken db path: /databases/kraken2/k2_standard_20240605

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata
  • summary.jsondata · 4 KB
  • taxonomic_report.htmlreport · 6 KB
  • top_taxa.tsvTSV · 590 B

Results

No static figure could be embedded in this notebook — this run recorded no PNG/SVG output, and no interactive plot could be exported to a static image. Any figures this run produced are listed among the raw artifacts below and remain viewable in the project itself.

Raw artifacts

22 output files produced across all stages (331.2 MB total). This report is self-contained; structures and trajectories are listed below for reference.