Metagenome Taxonomic Profiling | Skills PoolMetagenome Taxonomic Profiling
Profile microbial community composition from shotgun metagenomic reads using Kraken2/Bracken or MetaPhlAn 4.
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.
- 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
- If Kraken2: run
kraken2 with --report to generate a Kraken-style taxonomic report.
- If Bracken: run
bracken on the Kraken2 report for abundance re-estimation at the specified taxonomic level.
- If MetaPhlAn: run
metaphlan with --input_type fastq to produce a merged abundance table.
- Parse reports: extract top N taxa, relative abundances, and compute diversity metrics (Shannon, Simpson).
- 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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Use When