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
Convert Biom File to TSV file
Context
This tool converts BIOM format files into TSV format.
Since BIOM is a standard format in microbial ecology for storing abundance and taxonomy data,
converting it to TSV provides a more human-readable and widely compatible file for downstream processing, visualization, or integration with other tools.
It can also optionally include sequence information and multiple affiliation results.
How it does
The program takes an input BIOM file and extracts abundance data along with associated metadata.
If a FASTA file is provided, it appends the corresponding sequences to the output table.
When used with affiliations produced by FROGS, the script can generate a secondary output listing multiple hits or ambiguous affiliations.
It is straightforward to use and serves as a bridge between structured BIOM files and flexible tabular formats.
Configuration: 16S V3V4 Swarm
sbatch -J biom_to_tsv -o LOGS/biom_to_tsv.out -e LOGS/biom_to_tsv.err -c 8 --export=ALL --wrap="module load devel/Miniforge/Miniforge3 && module load bioinfo/FROGS/FROGS-v5.0.2 && biom_to_tsv.py --input-biom FROGS/SWARM/affiliation.biom --input-fasta FROGS/SWARM/filters.fasta --output-tsv FROGS/SWARM/affiliation.tsv --output-multi-affi FROGS/SWARM/multi_aff.tsv --log-file FROGS/SWARM/biom_to_tsv.log && module unload bioinfo/FROGS/FROGS-v5.0.2"
biom_to_tsv.py --help)
Interpretation: 16S V3V4 Swarm
Here are the results for our clusters, quite a few of them are multi-affiliated:
FROGS uses blast tool against a reference databank to assign clusters. Particularly with 16S amplicon data, different species can harbor a similar, or even identical, 16S sequence in the targeted region. This is a very common phenomenon which explains why 16S analyses often do not discriminate between species within the same Genus. FROGS gives you the ability to view the conflicting affiliations of a given cluster. These are called multi-affiliations. Here is an example of a multi-affiliation.
FROGS uses blast tool against a reference databank to assign clusters. Particularly with 16S amplicon data, different species can harbor a similar, or even identical, 16S sequence in the targeted region. This is a very common phenomenon which explains why 16S analyses often do not discriminate between species within the same Genus. FROGS gives you the ability to view the conflicting affiliations of a given cluster. These are called multi-affiliations. Here is an example of a multi-affiliation.