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
ITSx : extract ITS region
Context
This is a bioinformatics utility designed to process Internal Transcribed Spacer (ITS) sequences, mainly from fungi. ITS regions are widely
used in microbial ecology and taxonomy as genetic markers. This tool identifies and extracts ITS subregions (ITS1 or ITS2), filters out non-ITS
sequences, and helps improve the quality of downstream analyses by cleaning the input data. It is often used in fungal community studies where
ITS sequencing is the standard marker for diversity and taxonomy profiling.
How it does
The tool scans the input FASTA sequences and, depending on the specified parameters, checks whether they correspond to ITS regions. It can focus on
specific organism groups (defaulting to fungi) and trim the sequences to the chosen ITS region (ITS1 or ITS2). The process can run in parallel using
multiple CPUs. If provided with both FASTA sequences and an abundance BIOM file, the program removes non-ITS or chimeric sequences and updates the
abundance information accordingly. Users can also run a simple validation mode (--check-its-only) to verify if sequences belong to ITS regions without
trimming them.
Configuration: Short reads (ITS use cases)
sbatch -J itsx -o LOGS/itsx.out -e LOGS/itsx.err -c 8 --export=ALL --wrap="module load devel/Miniforge/Miniforge3 && module load bioinfo/FROGS/FROGS-v5.0.2 && itsx.py --input-fasta FROGS/ITS/filters.fasta --input-biom FROGS/ITS/filters.biom --organism-groups 'F' --check-its-only --output-fasta FROGS/ITS/itsx.fasta --output-removed-sequences FROGS/ITS/removed_itsx.fasta --output-biom FROGS/ITS/itsx.biom --html FROGS/ITS/itsx.html && module unload bioinfo/FROGS/FROGS-v5.0.2"
itsx.py --help)
Interpretation: Short reads (ITS use cases)
Let look at the HTML file to see the result of ITSx.
This report allows to show the impact of our filters: