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
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
pipeline command, as a flowchart:
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.