RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data
Summary: 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 li...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-11-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222015619 |
| _version_ | 1811192530686967808 |
|---|---|
| author | Renata Kabiljo Harry Bowles Heather Marriott Ashley R. Jones Clement R. Bouton Richard J.B. Dobson John P. Quinn Ahmad Al Khleifat Chad M. Swanson Ammar Al-Chalabi Alfredo Iacoangeli |
| author_facet | Renata Kabiljo Harry Bowles Heather Marriott Ashley R. Jones Clement R. Bouton Richard J.B. Dobson John P. Quinn Ahmad Al Khleifat Chad M. Swanson Ammar Al-Chalabi Alfredo Iacoangeli |
| author_sort | Renata Kabiljo |
| collection | DOAJ |
| description | Summary: 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. |
| first_indexed | 2024-04-11T23:54:08Z |
| format | Article |
| id | doaj.art-6fd85c92a4d0435a9afd0120daad3959 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-04-11T23:54:08Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-6fd85c92a4d0435a9afd0120daad39592022-12-22T03:56:24ZengElsevieriScience2589-00422022-11-012511105289RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing dataRenata Kabiljo0Harry Bowles1Heather Marriott2Ashley R. Jones3Clement R. Bouton4Richard J.B. Dobson5John P. Quinn6Ahmad Al Khleifat7Chad M. Swanson8Ammar Al-Chalabi9Alfredo Iacoangeli10Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK; Corresponding authorDepartment of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UKDepartment of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UKDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UKDepartment of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UKDepartment of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK; NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK; Institute of Health Informatics, University College London, London, UK; NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London, UKDepartment of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UKDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UKDepartment of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UKDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UKDepartment of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK; Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK; NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004222015619BioinformaticsBiocomputational methodSequence analysis |
| spellingShingle | Renata Kabiljo Harry Bowles Heather Marriott Ashley R. Jones Clement R. Bouton Richard J.B. Dobson John P. Quinn Ahmad Al Khleifat Chad M. Swanson Ammar Al-Chalabi Alfredo Iacoangeli RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data iScience Bioinformatics Biocomputational method Sequence analysis |
| title | RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data |
| title_full | RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data |
| title_fullStr | RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data |
| title_full_unstemmed | RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data |
| title_short | RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data |
| title_sort | retrosnake a modular pipeline to detect human endogenous retroviruses in genome sequencing data |
| topic | Bioinformatics Biocomputational method Sequence analysis |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222015619 |
| work_keys_str_mv | AT renatakabiljo retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT harrybowles retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT heathermarriott retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT ashleyrjones retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT clementrbouton retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT richardjbdobson retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT johnpquinn retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT ahmadalkhleifat retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT chadmswanson retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT ammaralchalabi retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata AT alfredoiacoangeli retrosnakeamodularpipelinetodetecthumanendogenousretrovirusesingenomesequencingdata |