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Scientific-ToolingScientific-Tooling/structured-intelligence/skills/metagenome-taxonomic-profiling/SKILL.md

metagenome-taxonomic-profiling

Skill4 starsChanged 12 days agoMITView on GitHub

Profile microbial community composition from shotgun metagenomic reads using Kraken2/Bracken or MetaPhlAn 4.

The file

We split this skill into the rules it gives an agent

3 rules. About 0 are common, 0 are distinctive, and 3 are very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈0

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 3

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Very specific:

    If Kraken2: run kraken2 with --report to generate a Kraken-style taxonomic report.

    line 31
  2. Very specific:

    If Bracken: run bracken on the Kraken2 report for abundance re-estimation at the specified taxonomic level.

    line 32
  3. Very specific:

    If MetaPhlAn: run metaphlan with --input_type fastq to produce a merged abundance table.

    line 33

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

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Files
SKILL.md

Skill: metagenome-taxonomic-profiling

Use When

  • The user wants to determine which organisms are present in a metagenomic sample.
  • The user needs taxonomic abundance estimates at species, genus, or phylum level.
  • The user wants to compare Kraken2 vs MetaPhlAn profiling approaches.
  • The user needs Bracken re-estimation for more accurate species-level abundance from Kraken2 output.

Inputs

  • Required:
    • Host-depleted FASTQ file(s) (.fastq, .fq, .fastq.gz, .fq.gz).
  • Optional:
    • --profiler STR — Profiler to use: kraken2 or metaphlan (default: kraken2).
    • --db PATH — Kraken2 or MetaPhlAn database path.
    • --bracken-db PATH — Bracken database path (for Bracken re-estimation).
    • --bracken-len N — Read length for Bracken (e.g., 100, 150, 250).
    • --level CHAR — Taxonomic level for Bracken: S (species), G (genus), P (phylum), etc. (default: S).
    • --threads N — Number of threads (default: 4).
    • --outdir DIR — Output directory (default: taxonomic_profiling_results).
    • --confidence FLOAT — Kraken2 confidence threshold (default: 0.0).

Workflow

  1. If Kraken2: run kraken2 with --report to generate a Kraken-style taxonomic report.
  2. If Bracken: run bracken on the Kraken2 report for abundance re-estimation at the specified taxonomic level.
  3. If MetaPhlAn: run metaphlan with --input_type fastq to produce a merged abundance table.
  4. Parse reports: extract top N taxa, relative abundances, and compute diversity metrics (Shannon, Simpson).
  5. Report: classification rate, top taxa, total species detected, alpha diversity estimates.

Output Contract

  • Kraken2 report — Standard Kraken2 taxonomic report (<outdir>/<sample>_kraken2_report.txt).
  • Bracken abundance table — Re-estimated abundances at the specified level (<outdir>/<sample>_bracken.txt), if Bracken is used.
  • MetaPhlAn profile — Relative abundance table (<outdir>/<sample>_metaphlan_profile.txt), if MetaPhlAn is used.
  • Classification rate — Percentage of reads assigned to a taxon.
  • Top taxa summary — Top 20 taxa by relative abundance.
  • Diversity metrics — Shannon and Simpson alpha diversity indices.

Limits

  • Kraken2 standard database is approximately 70 GB and requires sufficient RAM to load into memory.
  • MetaPhlAn 4 uses marker genes; it has a smaller database and higher species-level precision but may miss novel taxa without markers.
  • Bracken requires a pre-built Bracken database matching the Kraken2 database and the read length used in sequencing.
  • Kraken2 and MetaPhlAn must be installed and available on $PATH.
  • Classification rates vary significantly by database completeness and sample type.
  • For low-biomass samples, consider using a higher Kraken2 confidence threshold to reduce false positives.
  • Common failure cases:
    • Kraken2 database too large to fit in available RAM, causing out-of-memory crash.
    • Bracken database read length not matching actual sequencing read length.
    • MetaPhlAn marker database version incompatible with the installed MetaPhlAn version.

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