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.

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.

Select the Optional 2. ITSx tool.



This tool is typically used after cluster filters. Files are detected automatically, please verify that these are the correct files.



We want to keep conserved regions, click on No .



The organisms we are interested in are Fungi.



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