D
Donovan H. Parks
Researcher at University of Queensland
Publications - 85
Citations - 42111
Donovan H. Parks is an academic researcher from University of Queensland. The author has contributed to research in topics: Genome & Metagenomics. The author has an hindex of 38, co-authored 77 publications receiving 29033 citations. Previous affiliations of Donovan H. Parks include Dalhousie University & University of British Columbia.
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
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STAMP: statistical analysis of taxonomic and functional profiles
TL;DR: UNLABELLED STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles and a user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots.
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Donovan H. Parks,Maria Chuvochina,David W. Waite,Christian Rinke,Adam Skarshewski,Pierre-Alain Chaumeil,Philip Hugenholtz +6 more
TL;DR: This work used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence.
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
TL;DR: The accuracy of the GTDB-Tk taxonomic assignments is demonstrated by evaluating its performance on a phylogenetically diverse set of 10 156 bacterial and archaeal metagenome-assembled genomes.