RetroSnake: a Modular Pipeline for Detection of Human Endogenous Retroviruses in Genome Sequencing data

Renata Kabiljo; Harry Bowles; Heather Marriott; Ashley R. Jones; Clement R. Bouton; Richard JB. Dobson; John P. Quinn; Ahmad Al Khleifat; Chad M. Swanson; Ammar Al-Chalabi; Alfredo Iacoangeli

doi:10.1016/j.isci.2022.105289

RetroSnake: a Modular Pipeline for Detection of Human Endogenous Retroviruses in Genome Sequencing data

Renata Kabiljo^*, Harry Bowles, Heather Marriott, Ashley R. Jones, Clement R. Bouton, Richard JB. Dobson, John P. Quinn, Ahmad Al Khleifat, Chad M. Swanson, Ammar Al-Chalabi, Alfredo Iacoangeli^*

^*Corresponding author for this work

University of Liverpool

Research output: Contribution to journal › Article › peer-review

Abstract

Human Endogenous Retroviruses (HERVs) integrated into the genome of vertebrates 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 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 discovery 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 customisable 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.

Original language	English
Pages (from-to)	105289
Journal	iScience
DOIs	https://doi.org/10.1016/j.isci.2022.105289
Publication status	Accepted/In press - 4 Oct 2022

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title = "RetroSnake: a Modular Pipeline for Detection of Human Endogenous Retroviruses in Genome Sequencing data",

abstract = "Human Endogenous Retroviruses (HERVs) integrated into the genome of vertebrates 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 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 discovery 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 customisable 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.",

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AU - Kabiljo, Renata

AU - Bowles, Harry

AU - Marriott, Heather

AU - Jones, Ashley R.

AU - Bouton, Clement R.

AU - Dobson, Richard JB.

AU - Quinn, John P.

AU - Al Khleifat, Ahmad

AU - Swanson, Chad M.

AU - Al-Chalabi, Ammar

AU - Iacoangeli, Alfredo

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AB - Human Endogenous Retroviruses (HERVs) integrated into the genome of vertebrates 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 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 discovery 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 customisable 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.

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JO - iScience

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ER -

RetroSnake: a Modular Pipeline for Detection of Human Endogenous Retroviruses in Genome Sequencing data

Abstract

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