LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

Al Qaffas, A., Nichols, J. , Davison, A. J. , Ourahmane, A., Hertel, L., McVoy, M. A. and Camiolo, S. (2021) LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data. Virus Evolution, 7(1), veab042. (doi: 10.1093/ve/veab042)

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Abstract

Long-read, single-molecule DNA sequencing technologies have triggered a revolution in genomics by enabling the determination of large, reference-quality genomes in ways that overcome some of the limitations of short-read sequencing. However, the greater length and higher error rate of the reads generated on long-read platforms make the tools used for assembling short reads unsuitable for use in data assembly, and motivate the development of new approaches. We present LoReTTA, a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. The tool was designed to deal with reads originating from viral genomes, which feature high genetic variability, possible multiple isoforms and the dominant presence of additional organisms in clinical or environmental samples. LoReTTA was tested on a range of simulated and experimental datasets, and outperformed established long-read assemblers in terms of assembly contiguity and accuracy. The software runs under the Linux operating system, is designed for easy adaptation to alternative systems, and features an automatic installation pipeline that takes care of the required dependencies. A command-line version and a user-friendly graphical interface version are available under a GPLv3 license 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 Nichols, Mrs Jenna and Davison, Professor Andrew
Authors: Al Qaffas, A., Nichols, J., Davison, A. J., Ourahmane, A., Hertel, L., McVoy, M. A., and Camiolo, S.
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:23 April 2021
Copyright Holders:Copyright © 2021 The Authors
First Published:First published in Virus Evolution 7(1): veab042
Publisher Policy:Reproduced under a Creative Commons licence

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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
Medical Research Council (MRC)MC_UU_12014/3