[en] 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.
Disciplines :
Genetics & genetic processes
Author, co-author :
Chitneedi, Praveen Krishna ; Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany ; Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Hadlich, Frieder; Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
Moreira, Gabriel C. M.; Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium
Espinosa-Carrasco, Jose ; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
Li, Changxi; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada ; Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Canada
Plastow, Graham ; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
Fischer, Daniel; Natural Resources Institute Finland (Luke), Green Technology, Animal and Plant Genomics and Breeding, Jokioinen, Finland
Charlier, Carole ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics
Rocha, Dominique; Universite Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
Chamberlain, Amanda J.; Agriculture Victoria Research, AgriBio, Centre for AgriBiosciences, Bundoora, Australia ; School of Applied Systems Biology, La Trobe University, Bundoora, Australia
Kuehn, Christa; Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany ; Faculty of Agricultural and Environmental Science, University Rostock, Rostock, Germany ; Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald, Germany
Language :
English
Title :
EQTL-Detect: Nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts
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