metagenomics

Metagenomics

Version Compatibility

Reference examples assume:

• fastp 0.23+
• kraken2 2.1+
• bracken 2.8+
• metaphlan 4+
• humann 3.9+

Verify the environment first:

• CLI: kraken2 --version, bracken -v, metaphlan --version, humann --version

Overview

Use this skill for shotgun metagenomics when the user needs:

• QC and host depletion review
• taxonomic abundance tables
• functional pathway profiles
• AMR or strain-level follow-up

When To Use This Skill

• the data are shotgun metagenomics rather than amplicon sequencing
• the user wants species or genus abundances, function, or resistance summaries
• multiple samples need cohort-level comparison

Quick Route

• host-associated samples: perform host depletion before interpretation
• taxonomy only: kraken2 + bracken is a common pragmatic route
• function only or plus taxonomy: add humann
• strain claims require more evidence than top-level taxonomy calls

Progressive Disclosure

• Read technical_reference.md for database choice, host contamination review, and functional profiling caveats.
• Read commands_and_thresholds.md for command-line patterns, thresholds, and output layout.

Expected Inputs

• paired or single-end metagenomic FASTQ
• sample metadata
• taxonomy and optional function databases

Expected Outputs

• results/taxonomy/bracken_species.tsv
• results/taxonomy/bracken_genus.tsv
• results/function/pathabundance.tsv
• results/amr/amr_summary.tsv
• qc/read_processing_summary.tsv

Starter Pattern

fastp \
  -i sample_R1.fastq.gz \
  -I sample_R2.fastq.gz \
  -o qc/sample.clean.R1.fastq.gz \
  -O qc/sample.clean.R2.fastq.gz \
  --html qc/sample.fastp.html \
  --json qc/sample.fastp.json

kraken2 \
  --db $KRAKEN_DB \
  --paired qc/sample.clean.R1.fastq.gz qc/sample.clean.R2.fastq.gz \
  --report results/taxonomy/sample.kraken.report \
  --output results/taxonomy/sample.kraken.out \
  --confidence 0.1