UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

Kamrad, S; Rodríguez-López, M; Cotobal, C; Correia-Melo, C; Ralser, M; Bähler, J; (2020) Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens. Elife , 9 , Article e55160. 10.7554/eLife.55160. Green open access

[thumbnail of elife-55160-v1.pdf]
Preview
Text
elife-55160-v1.pdf - Published Version

Download (2MB) | Preview

Abstract

Microbial fitness screens are a key technique in functional genomics. We present an allin-one solution, pyphe, for automating and improving data analysis pipelines associated with largescale fitness screens, including image acquisition and quantification, data normalisation, and statistical analysis. Pyphe is versatile and processes fitness data from colony sizes, viability scores from phloxine B staining or colony growth curves, all obtained with inexpensive transilluminating flatbed scanners. We apply pyphe to show that the fitness information contained in late endpoint measurements of colony sizes is similar to maximum growth slopes from time series. We phenotype gene-deletion strains of fission yeast in 59,350 individual fitness assays in 70 conditions, revealing that colony size and viability provide complementary, independent information. Viability scores obtained from quantifying the redness of phloxine-stained colonies accurately reflect the fraction of live cells within colonies. Pyphe is user-friendly, open-source and fully documented, illustrated by applications to diverse fitness analysis scenarios.

Type: Article
Title: Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.7554/eLife.55160
Publisher version: https://doi.org/10.7554/eLife.55160
Language: English
Additional information: This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. http://creativecommons.org/licenses/by/4.0/
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10102781
Downloads since deposit
63Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item