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) (PMID:33996146) (PMCID:PMC8111061)
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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: | Davison, Professor Andrew and Nichols, Mrs Jenna and Camiolo, Dr Salvatore |
| 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 > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| 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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