FROGS Core
Galaxy
- Get Started ▾
- Reads processing
- Remove chimera
- Cluster/ASV filters
- Taxonomic affiliation
- Phylogenetic tree building
- ITSx
- Read demultiplexing
- Affiliatio filters
- Affiliation postprocessing
- Abundance normalisation
- Convert Biom file to TSV file
- Convert TSV file to Biom file
- Cluster/ASV report
- Affiliation report
Main tools
Optional tools
CLI
- Get Started
- Reads processing
- Remove chimera
- Cluster/ASV filters
- Taxonomic affiliation
- Phylogenetic tree building
- ITSx
- Read demultiplexing
- Affiliation filters
- Affiliation postprocessing
- Abundance normalisation
- Convert Biom file to TSV file
- Convert TSV file to Biom file
- Cluster/ASV report
- Affiliation report
Main tools
Optional tools
Affiliation postprocessing
Context
This is a post-processing tool used in microbial community analysis pipelines (e.g., after ASV detection and taxonomic affiliation).
Its main purpose is to refine taxonomic affiliations by:
Detecting and resolving nested amplicons (ASVs fully contained within longer sequences).
Aggregating redundant ASVs that have identical or very similar affiliations, avoiding overrepresentation of biologically similar sequences.
This is especially important when analyzing 16S rRNA gene data, where overlapping amplicons or highly similar ASVs can artificially inflate diversity.
How it does
It compares ASVs based on :
- Sequence identity
- Alignment coverage
Configuration: 16S V3V4 Swarm
Refine affiliations, to manage amplicon included in other sequence, and to
deal with surnumerary ASV (ASV with same affiliations).
sbatch -J a_postprocess -o LOGS/affiliation_postprocess.out -e LOGS/affiliation_postprocess.err -c 8 --export=ALL --wrap="module load devel/Miniforge/Miniforge3 && module load bioinfo/FROGS/FROGS-v5.0.2 && affiliation_postprocess.py --input-fasta FROGS/SWARM/filters.fasta --input-biom FROGS/SWARM/affiliation.biom --log-file FROGS/SWARM/affiliation_postprocess.log --output-biom FROGS/SWARM/affiliation_postprocess.biom --output-fasta FROGS/SWARM/affiliation_postprocess.fasta --identity 98 --coverage 98 && module unload bioinfo/FROGS/FROGS-v5.0.2"
affiliation_postprocess.py --help)