Package: thapbi-pict
THAPBIPhytophthoraITS1 Classifier Tool (PICT)AboutTHAPBI 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 identifyingPhytophthoraspecies 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 justPhytophthoraITS1. It requires overlapping paired-end Illumina
reads which can be merged to cover thefullamplicon 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.InstallationWe recommend installing this tool on Linux or macOS using theCondapackaging system, via theBioCondachannel, which will handleallthe dependencies:$condainstallthapbi-pictAlternatively or on Windows, sincethe software is on the Python Package
Index (PyPI), the following command
will install it along with its Python dependencies:$pipinstallthapbi-pictHowever, in this case you will still need to install various external command
line tools. SeeINSTALL.rstfor more details (especially for Windows),
and if you want to modify the software readCONTRIBUTING.rstas well.Quick StartOnce installed, you should be able to run the tool at the command line
using:$thapbi_pictThis should automatically find the installed copy of the Python code.
Usethapbi_pict-vto report the version, orthapbi_pict-hfor
help.DocumentationThetool documentationis hosted byRead The Docs, generated automatically from thedocs/folder.The documentation includes more detailed discussion of the sample datasets
in theexamples/folder (which are based on published datasets).CitationIf you use THAPBI PICT in your work, please cite ourPeerJpaper, and give
details of the version and any non-default settings used in your methods:Cocket al.(2023) “THAPBI PICT - a fast, cautious, and accurate
metabarcoding analysis pipeline”PeerJ11:e15648https://doi.org/10.7717/peerj.15648You can also cite the software specifically via Zenodo which offers version
specific DOIs as well ashttps://doi.org/10.5281/zenodo.4529395which is for
the latest version.FundingThe 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)
andScottish Government, under the Tree
Health and Plant Biosecurity Initiative, grant numberBB/N023463/1.Work from 2020 to 2021 was supported in part under theEarly 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.BackgroundTHAPBI PICT continues earlier work including:https://github.com/widdowquinn/THAPBIhttps://github.com/widdowquinn/THAPBI-pycitshttps://github.com/peterthorpe5/THAPBI-pycitshttps://github.com/peterthorpe5/public_scripts/tree/master/metapyhttps://github.com/peterthorpe5/public_scripts/tree/master/metapy_toolsRelease HistorySee theCHANGELOG.rstfile.Development NotesSee fileCONTRIBUTING.rstfor details of the development setup including
Python style conventions, git pre-commit hook, continuous integration and test
coverage, and release process.