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THAPBI Phytophthora ITS1 Classifier Tool (PICT).

Project description

THAPBI PICT on the Python Package Index (PyPI) THAPBI PICT on BioConda THAPBI PICT TravisCI build status THAPBI PICT CircleCI build status Documentation Status Code style: black

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, focused on identifying Phytophthora species present in Illumina sequenced environmental samples.

Phytophthora (from Greek meaning plant-destroyer) species are economically important plant pathogens, important 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, 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.

The worked examples include oomycetes, fungi, microalgae, and bats, and cover markers in ITS1, ITS2, 18S rRNA and COI and more. The main criteria has been mock communities with known species composition.


We recommend installing this tool on Linux or macOS using the Conda packaging system, via the BioConda channel, which will handle all the dependencies:

$ conda install thapbi_pict

Sadly the command line dependencies likely rule out using Windows directly.

Alternatively, since the software is on the Python Package Index (PyPI), the following command will install it along with its Python dependencies:

$ pip install thapbi_pict

However, in this case you will still need to install various external command line tools. See INSTALL.rst for more details, and if you want to modify the software read CONTRIBUTING.rst as well.

Quick Start

Once installed, you should be able to run the tool at the command line using:

$ thapbi_pict

This should automatically find the installed copy of the Python code. Use thapbi_pict -v to report the version, or thapbi_pict -h for help.


The tool documentation is hosted by Read The Docs, generated automatically from the docs/ folder.

The documentation includes more detailed discussion of the sample datasets in the examples/ folder (which are based on published datasets).


The Phyto-Threats project was supported from 2016 to 2019 under the Tree Health and Plant Biosecurity Initiative (THAPBI), jointly funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Department for Environment, Food and Rural affairs (DEFRA), Economic and Social Research Council (ESRC), Forestry Commission, Natural Environment Research Council (NERC) and Scottish Government.

Release History

See the CHANGELOG.rst file.

Development Notes

Please see the CONTRIBUTING.rst file for details of the development setup including Python style conventions, git pre-commit hook, continuous integration and test coverage, and release process.

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