Group Software
Group Software
We write and maintain a number of scripts, packages, and other tools to aid in our research and teaching. The great majority of the software we write is released under open licences, such as the MIT Licence or CC-BY-SA. Some of this software is described below.
pyani
pyani is an application for scalable whole-genome classification of microbes using Average Nucleotide Identity
CITATION: Pritchard et al. (2016) “Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens” Anal. Methods 8, 12-24 doi:10.1039/C5AY02550H
cazy_webscraper
cazy_webscraper is a program that retrieves data from the CAZy database and stores it locally in a database format for fast and powerful querying.
ncfp
ncfp is a command-line tool intended to facilitate phylogenetic tree reconstruction that retrieves corresponding nucleotide coding sequecnes for a set of input protein sequences, from NCBI. ncfp can retrieve complete coding sequences or domain fragments (using the appropriate domain format).
pdp
pdp is an application for the automated design of primers for molecular diagnostics, including qPCR and metabarcoding. Given a set of input genomes with corresponding classifications (e.g. pathogenic and non-pathogenic) it can design candidate primer sets for regions diagnostic to each class, enabling amplification of characteristic regions. For metabarcoding, it can identify regions with maximal amplicon sequence diversity (including variation below species-level) to aid more accurate estimation of population diversity.
Group GitHub Pages
GitHub pages for current and former group members include:
