Environmental Phytophthora ITS1

This example is based on the following paper from earlier in the THAPBI Phyto-Threats project, where the original analysis used the precursor pipeline metapy:

Riddell et al. (2019) Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain. https://doi.org/10.7717/peerj.6931

Importantly, they used the same PCR primers, and therefore analysis with this tool’s default settings including the provided database is appropriate.

The Quick Start described a simplified use of the THAPBI PICT tool to assess a single Illumina MiSeq sequencing run using the thapbi_pict pipeline command, as a flowchart:

Flowchart summarising THAPBI PICT pipeline, from raw paired FASTQ files to reports, using metadata.

Here we will run over the same process using real Phytophthora ITS1 data, calling the individual commands within the default pipeline - and include metadata for reporting. We then run the equivalent all-in-one pipeline command.

Finally, since the sample data includes some positive controls, we can look at assessing the classifier performance.