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RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data

Kabiljo, R; Bowles, H; Marriott, H; Jones, AR; Bouton, CR; Dobson, RJB; Quinn, JP; ... Iacoangeli, A; + view all (2022) RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data. iScience , 25 (11) , Article 105289. 10.1016/j.isci.2022.105289. Green open access

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Abstract

Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training. Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.

Type: Article
Title: RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.isci.2022.105289
Publisher version: https://doi.org/10.1016/j.isci.2022.105289
Language: English
Additional information: Copyright © 2022 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Keywords: Biocomputational method, Bioinformatics, Sequence analysis
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 Population Health Sciences > Institute of Health Informatics
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute of Health Informatics > Clinical Epidemiology
URI: https://discovery.ucl.ac.uk/id/eprint/10160153
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