thapbi-pict 1.0.17

THAPBI Phytophthora ITS1 Classifier Tool (PICT).

THAPBI Phytophthora ITS1 Classifier Tool (PICT)

About

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.

Installation

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

Alternatively or on Windows, 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 (especially for Windows), 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.

Documentation

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).

Citation

If you use THAPBI PICT in your work, please cite our PeerJ paper, and give details of the version and any non-default settings used in your methods:

Cock et al. (2023) “THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline” PeerJ 11:e15648 https://doi.org/10.7717/peerj.15648

You can also cite the software specifically via Zenodo which offers version specific DOIs as well as https://doi.org/10.5281/zenodo.4529395 which is for the latest version.

Funding

The initial work was supported from 2016 to 2019 under the Tree Health and Plant Biosecurity Initiative (THAPBI) Phyto-Threats project:

This research was supported by a grant funded jointly 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, under the Tree Health and Plant Biosecurity Initiative, grant number BB/N023463/1.

Work from 2020 to 2021 was supported in part under the Early detection of Phytophthora in EU and third country nurseries and traded plants (ID-PHYT) Euphresco project:

Funded by DEFRA as part of the Future Proofing Plant Health project in support of Euphresco ID-PHYT.

Work from 2022 to 2027 was partly funded by the Rural & Environment Science & Analytical Services (RESAS) Division of the Scottish Government.

Background

THAPBI PICT continues earlier work including:

• https://github.com/widdowquinn/THAPBI

• https://github.com/widdowquinn/THAPBI-pycits

• https://github.com/peterthorpe5/THAPBI-pycits

• https://github.com/peterthorpe5/public_scripts/tree/master/metapy

• https://github.com/peterthorpe5/public_scripts/tree/master/metapy_tools

Release History

See the CHANGELOG.rst file.

Development Notes

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