ArticlePeerJ2015
The impact of Docker containers on the performance of genomic pipelines.
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Establishment of the endocrine variant extractor and its clinical application in identifying a novelFrontiers in endocrinology · 2026Article
- MTBseq-nf: Enabling Scalable Tuberculosis Genomics "Big Data" Analysis Through a User-Friendly Nextflow Wrapper for MTBseq Pipeline.Microorganisms · 2025Article
- DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments.Biology · 2024Article
- Churros: a Docker-based pipeline for large-scale epigenomic analysis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- The five pillars of computational reproducibility: bioinformatics and beyond.Briefings in bioinformatics · 2023Article
- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- Artificial intelligence and machine learning in cancer imaging.Communications medicine · 2022Review
- VenomFlow: An Automated Bioinformatic Pipeline for Identification of Disulfide-Rich Peptides from Venom Arsenals.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences.GigaScience · 2021Article
- Design considerations for workflow management systems use in production genomics research and the clinic.Scientific reports · 2021Article
- Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging.Frontiers in genetics · 2021Review
- Cloud Computing Enabled Big Multi-Omics Data Analytics.Bioinformatics and biology insights · 2021Review
- The Stroke Neuro-Imaging Phenotype Repository: An Open Data Science Platform for Stroke Research.Frontiers in neuroinformatics · 2021Article
- Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity.BMC genomics · 2020Article
- MutantHuntWGS: A Pipeline for IdentifyingG3 (Bethesda, Md.) · 2020Article
- Article
- A Guide and Toolbox to Replicability and Open Science in Entomology.Journal of insect science (Online) · 2020Review
- Modeling population heterogeneity from microbial communities to immune response in cells.Cellular and molecular life sciences : CMLS · 2020Review
- NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly.BMC bioinformatics · 2019Article
- Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection.GigaScience · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. Docker containers are emerging as a possible solution for many of these problems, as they allow the packaging of pipelines in an isolated and self-contained manner. This makes it easy to distribute and execute pipelines in a portable manner across a wide range of computing platforms. Thus, the question that arises is to what extent the use of Docker containers might affect the performance of these pipelines. Here we address this question and conclude that Docker containers have only a minor impact on the performance of common genomic pipelines, which is negligible when the executed jobs are long in terms of computational time.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.