eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

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• dc.contributor.author Chitneedi, Praveen Krishna
• dc.contributor.author Hadlich, Frieder
• dc.contributor.author Moreira, Gabriel C. M.
• dc.contributor.author Espinosa-Carrasco, José
• dc.contributor.author Li, Changxi
• dc.contributor.author Plastow, Graham
• dc.contributor.author Fischer, Daniel
• dc.contributor.author Charlier, Carole
• dc.contributor.author Rocha, Dominique
• dc.contributor.author Chamberlain, Amanda J.
• dc.contributor.author Kuehn, Christa
• dc.date.accessioned 2024-12-09T07:18:28Z
• dc.date.available 2024-12-09T07:18:28Z
• dc.date.issued 2024
• dc.description.abstract Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow managers such as Nextflow provide a framework to overcome respective problems. This study used Nextflow to develop a bioinformatic pipeline for detecting expression quantitative trait loci (eQTL) using a DSL2 Nextflow modular syntax, to enable sharing the huge demand for computing power as well as data access limitation across different partners often associated with eQTL studies. Based on the results from a test run with pilot data by measuring the required runtime and computational resources, the new pipeline should be suitable for eQTL studies in large scale analyses.
• dc.description.sponsorship European Union's Horizon 2020 research and innovation programme under grant agreement No. 815668.
• dc.format.mimetype application/pdf
• dc.identifier.citation Chitneedi PK, Hadlich F, Moreira GCM, Espinosa-Carrasco J, Li C, Plastow G, et al. eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts. NAR Genom Bioinform. 2024 Sep 24;6(3):lqae122. DOI: 10.1093/nargab/lqae122
• dc.identifier.doi http://dx.doi.org/10.1093/nargab/lqae122
• dc.identifier.issn 2631-9268
• dc.identifier.uri http://hdl.handle.net/10230/68936
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof NAR Genom Bioinform. 2024 Sep 24;6(3):lqae122
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/815668
• dc.rights © The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.other Bioinformàtica
• dc.title eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion