THAPBI Phytophthora ITS1 Classifier Tool (PICT)
THAPBI PICT is a sequence based diagnostic/profiling tool from the UK funded Tree Health and Plant Biosecurity Initiative (THAPBI) Phyto-Threats project, initially focused on identifying Phytophthora species present in Illumina sequenced environmental samples.
Phytophthora (from Greek meaning plant-destroyer) species are economically important plant pathogens, in both agriculture and forestry. ITS1 is short for Internal Transcribed Spacer one, which is a region of eukaryotes genomes between the 18S and 5.8S rRNA genes. This is commonly used for molecular barcoding, where sequencing this short region can identify species.
With appropriate primer settings and a custom database of full length markers, THAPBI PICT can be applied to other organisms and/or barcode marker sequences - not just Phytophthora ITS1. It requires overlapping paired-end Illumina reads which can be merged to cover the full amplicon marker. Longer markers or fragmented amplicons are not supported. Internally it works by tracking unique amplicon sequence variants (ASVs), using MD5 checksums as identifiers.
The worked examples include oomycetes, fungi, fish, bats, and plants, and cover markers in ITS1, ITS2, 12S, 16S, COI, and more. The main criteria has been mock communities with known species composition.
The THAPBI Phyto-Threats project was initially supported by a grant funded jointly by the Biotechnology and Biological Sciences Research Council (BBSRC), the Department for Environment, Food and Rural affairs (DEFRA), the Economic and Social Research Council (ESRC), the Forestry Commission, the Natural Environment Research Council (NERC) and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative (THAPBI).
Documentation on Read The Docs: https://thapbi-pict.readthedocs.io/
Source code repository on GitHub: https://github.com/peterjc/thapbi-pict/
Software released on PyPI: https://pypi.org/project/thapbi-pict/
Zenodo DOI for software: https://doi.org/10.5281/zenodo.4529395
Paper on PeerJ: https://doi.org/10.7717/peerj.15648
This documentation was generated for THAPBI PICT version 1.0.4.