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DNAscan: personal computer compatible NGS analysis, annotation and visualisation.

Iacoangeli, A; Al Khleifat, A; Sproviero, W; Shatunov, A; Jones, AR; Morgan, SL; Pittman, A; Dobson, RJ; Newhouse, SJ; Al-Chalabi, A (2019) DNAscan: personal computer compatible NGS analysis, annotation and visualisation. BMC Bioinformatics, 20 (1). p. 213. ISSN 1471-2105 https://doi.org/10.1186/s12859-019-2791-8
SGUL Authors: Pittman, Alan Michael

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Abstract

BACKGROUND: Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range of uses exist, therefore it is challenging to design an analysis pipeline. Secondly, NGS analysis is computationally intensive, requiring expensive infrastructure, and many medical and research centres do not have adequate high performance computing facilities and cloud computing is not always an option due to privacy and ownership issues. Finally, the interpretation of the results is not trivial and most available pipelines lack the utilities to favour this crucial step. RESULTS: We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan . Instructions for an easy and fast deployment with Docker and Singularity are also provided on GitHub. CONCLUSIONS: DNAscan is an extremely fast and computationally efficient pipeline for analysis, visualization and interpretation of NGS data. It is designed to provide a powerful and easy-to-use tool for applications in biomedical research and diagnostic medicine, at minimal computational cost. Its comprehensive approach will maximise the potential audience of users, bringing such analyses within the reach of non-specialist laboratories, and those from centres with limited funding available.

Item Type: Article
Additional Information: © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords: Annotation, Bioinformatics, Next generation sequencing, Repeat expansion, Structural variants, Variant calling, Viral detection, Amyotrophic Lateral Sclerosis, Computational Biology, DNA, Bacterial, Databases, Factual, HIV-1, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation, Polymorphism, Single Nucleotide, RNA, Viral, User-Computer Interface, Whole Genome Sequencing, Humans, HIV-1, Amyotrophic Lateral Sclerosis, DNA, Bacterial, RNA, Viral, Computational Biology, Polymorphism, Single Nucleotide, User-Computer Interface, Databases, Factual, INDEL Mutation, High-Throughput Nucleotide Sequencing, Whole Genome Sequencing, 06 Biological Sciences, 08 Information And Computing Sciences, 01 Mathematical Sciences, Bioinformatics
SGUL Research Institute / Research Centre: Academic Structure > Molecular and Clinical Sciences Research Institute (MCS)
Journal or Publication Title: BMC Bioinformatics
ISSN: 1471-2105
Language: eng
Dates:
DateEvent
27 April 2019Published
2 April 2019Accepted
Publisher License: Creative Commons: Attribution 4.0
Projects:
Project IDFunderFunder ID
UNSPECIFIEDWellcome Trusthttp://dx.doi.org/10.13039/100004440
MR/L501529/1Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
MR/R024804/1Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
ES/L008238/1Economic and Social Research Councilhttp://dx.doi.org/10.13039/501100000269
633413Horizon 2020UNSPECIFIED
PubMed ID: 31029080
Go to PubMed abstract
URI: https://openaccess.sgul.ac.uk/id/eprint/110912
Publisher's version: https://doi.org/10.1186/s12859-019-2791-8

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