GRACy: a tool for analysing human cytomegalovirus sequence data

Camiolo, S. , Suárez, N. M., Chalka, A., Venturini, C., Breuer, J. and Davison, A. J. (2021) GRACy: a tool for analysing human cytomegalovirus sequence data. Virus Evolution, 7(1), veaa099. (doi: 10.1093/ve/veaa099)

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Abstract

Modern DNA sequencing has instituted a new era in human cytomegalovirus (HCMV) genomics. A key development has been the ability to determine the genome sequences of HCMV strains directly from clinical material. This involves the application of complex and often non-standardized bioinformatics approaches to analysing data of variable quality in a process that requires substantial manual intervention. To relieve this bottleneck, we have developed GRACy (Genome Reconstruction and Annotation of Cytomegalovirus), an easy-to-use tookit for analysing HCMV sequence data. GRACy automates and integrates modules for read filtering, genotyping, genome assembly, genome annotation, variant analysis and data submission. These modules were tested extensively on simulated and experimental data and outperformed generic approaches. GRACy is written in Python and is embedded in a graphical user interface with all required dependencies installed by a single command. It runs on the Linux operating system, and is designed to allow the future implementation of a cross-platform version. GRACy is distributed under a GPL 3.0 license and is freely available at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Camiolo, Dr Salvatore and Suarez, Dr Nicolas and Davison, Professor Andrew
Authors: Camiolo, S., Suárez, N. M., Chalka, A., Venturini, C., Breuer, J., and Davison, A. J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Virus Evolution
Publisher:Oxford University Press
ISSN:2057-1577
ISSN (Online):2057-1577
Published Online:30 December 2020
Copyright Holders:Copyright © 2020 The Authors
First Published:First published in Virus Evolution 7(1): veaa099
Publisher Policy:Reproduced under a Creative Commons License
Related URLs:

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
174258Exploiting a human challenge model to understand the pathogenesis of cytomegalovirusAndrew DavisonWellcome Trust (WELLCOTR)204870/Z/16/Z (17/0008)III-MRC-GU Centre for Virus Research