1. Taxonomic Profiling: Runs MetaPhlAn internally (or accepts precomputed profile) to identify present species.

2. Pangenome Mapping: Aligns reads against species-specific pangenome nucleotide databases using Bowtie2; quantifies known gene families with high precision.

3. Translated Search: Unmapped reads are aligned against UniRef protein databases using DIAMOND to capture divergent/novel functions.

4. Pathway Inference: Maps gene family abundances to MetaCyc pathways via MinPath, computing pathway coverage and abundance while minimizing false-positive pathway calls.

5. Stratification & Output: Generates stratified (per-species) and unstratified functional tables, normalized to CPM or relative abundance.

Data

SRR33039009_paired.fastq.gz

Results

SRR33039009_paired_genefamilies.tsv

SRR33039009_paired_pathabundance.tsv

Versions

v1.0: Process construction, complete the basic process of functional profiling.

Usage

1. Select the application 'Functional profiling'
2. Click on the 'Analysis' button
3. Click on the 'humann'
4. Click on the 'Add Option' to add fileName from self upload, and then fill in the request parameters

humann --input sample_R1.fq.gz,sample_R2.fq.gz --output humann_out --taxonomic-profile metaphlan_profile.tsv --threads 8 --memory-use maximum --normalization cpm --output-format tsv biom