Metagenomics Pipeline
metagenomicsTaxonomic profiling from shotgun metagenomic reads using MetaPhlAn or Kraken2.
The Metagenomics pipeline identifies and quantifies microbial taxa in shotgun sequencing data:
- **Quality control**: fastp trims and filters reads - **Profiling**: MetaPhlAn (default) or Kraken2 assigns reads to taxa - **Output**: Taxonomic profile, report, and fastp summary
Supports single-end or paired-end FASTQ. R1 can also be AB1/ABI (Sanger), which is converted to FASTQ automatically.
Reads (required)
- R1: FASTQ or AB1/ABI (AB1/ABI converted automatically) - R2 (optional): FASTQ for paired-end
Parameters
- **Classifier**: MetaPhlAn (default) or Kraken2 - **Kraken2 database**: Required if using Kraken2; path to pre-built DB - **Quality threshold**, **trimming window**, **threads**: Standard QC and compute options
- **Taxonomic profile**: Abundance table (species/strains for MetaPhlAn, or Kraken2 report) - **Report file**: Human-readable summary - **fastp report**: QC and trimming summary
1. For MetaPhlAn, no extra database is needed; it uses built-in marker DB 2. For Kraken2, use a pre-built standard or custom database 3. Paired-end reads generally improve classification accuracy 4. Check fastp for adapter contamination and read quality before interpreting profiles