RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.
Biocomputational method
Bioinformatics
Sequence analysis
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
18 Nov 2022
18 Nov 2022
Historique:
received:
03
03
2022
revised:
08
08
2022
accepted:
04
10
2022
entrez:
7
11
2022
pubmed:
8
11
2022
medline:
8
11
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 36339261
doi: 10.1016/j.isci.2022.105289
pii: S2589-0042(22)01561-9
pmc: PMC9626663
doi:
Types de publication
Journal Article
Langues
eng
Pagination
105289Subventions
Organisme : Medical Research Council
ID : MR/L501529/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S000844/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_17214
Pays : United Kingdom
Organisme : Alzheimer's Society
ID : 171
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R024804/1
Pays : United Kingdom
Organisme : Motor Neurone Disease Association
ID : ALCHALABI-DOBSON/APR14/829-791
Pays : United Kingdom
Informations de copyright
© 2022.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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