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 TSV file to BIOM file
Context
This is a conversion tool that transforms an abundance table in TSV format into a BIOM file.
BIOM is the standard format used in microbial ecology pipelines, allowing the storage of abundances, taxonomic metadata,
and sequence information in a structured way. This tool is especially useful to reintroduce manually processed or exported
TSV data back into a BIOM-compatible workflow.
How it does
The program parses the input TSV file that contains abundance data and metadata. If provided, it also integrates an additional
TSV file that holds information about multiple taxonomic affiliations, which can occur when sequences have ambiguous assignments.
Based on these inputs, the script reconstructs a BIOM file that preserves the hierarchical structure of taxonomies. If sequences
are included in the TSV under the
seed_sequence tag, the program can export them into a FASTA file.
Configuration: 16S V3V4 Swarm
sbatch -J tsv_to_biom -o LOGS/tsv_to_biom.out -e LOGS/tsv_to_biom.err -c 8 --export=ALL --wrap="module load devel/Miniforge/Miniforge3 && module load bioinfo/FROGS/FROGS-v5.0.2 && tsv_to_biom.py --input-tsv FROGS/SWARM/affiliation.tsv --input-multi-affi FROGS/SWARM/multi_aff.tsv --output-biom FROGS/SWARM/affiliation_bis.biom --output-fasta FROGS/SWARM/affiliation.fasta --log-file FROGS/SWARM/tsv_to_biom.log && module unload bioinfo/FROGS/FROGS-v5.0.2"
tsv_to_biom.py --help)