Worked Examples

While THAPBI PICT stands for Phytophthora ITS1 Classification Tool, with appropriate primer settings and a custom database, it can be applied to other organisms and/or barcode marker sequences.

These worked examples use public datasets from published papers, with various markers covering oomycetes, fungi, animals and plants. The main criteria has been mock communities with known species composition.

For each worked example there is a different sub-folder in the THAPBI PICT source code under examples/ containing at least to do one-off setup like downloading the public data, and to execute the main analysis discussed. There will usually be assorted other files like reference sequences, or metadata.tsv.

Running the examples will create or use subdirectories raw_data/ for the downloaded FASTQ files, intermediate/ for per-sample working files, and summary/ for the final output reports. Where the example includes positive controls like mock communities, the expected species content is recorded under expected/ in per-sample files.