ArticleBMC bioinformatics2016
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
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- UVA Irradiation Promotes ROS-Mediated Formation of the Common Deletion in Mitochondrial DNA.Life (Basel, Switzerland) · 2026Article
- Prion propagation is controlled by a hierarchical network involving the nuclear Tfap2c and hnRNP K factors and the cytosolic mTORC1 complex.PLoS pathogens · 2026Article
- Mechanical gating of tendon fibrogenic transcription in systemic sclerosis.Nature communications · 2026Article
- Article
- Dietary folic acid prevents peripheral neuropathy in mouse models of neural tube defects and type 2 diabetes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- IL-17-mediated antifungal immunity restricts Candida albicans pathogenicity in the oral cavity.Nature microbiology · 2026Article
- L-Phenylalanine is a metabolic checkpoint of human Th2 cells.Cell reports. Medicine · 2025Article
- Endometrial Stromal Cells from Endometriosis Patients Reflect Lesion-Type-Specific Heterogeneity.Cells · 2025Article
- Macrophages expressing chimeric cytokine receptors have an inflammatory phenotype and antitumoral activity upon IL-10 or TGFβ stimulation.Journal for immunotherapy of cancer · 2025Article
- Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing (NGS) produces massive datasets consisting of billions of reads and up to thousands of samples. Subsequent bioinformatic analysis is typically done with the help of open source tools, where each application performs a single step towards the final result. This situation leaves the bioinformaticians with the tasks to combine the tools, manage the data files and meta-information, document the analysis, and ensure reproducibility.
resultsWe present SUSHI, an agile data analysis framework that relieves bioinformaticians from the administrative challenges of their data analysis. SUSHI lets users build reproducible data analysis workflows from individual applications and manages the input data, the parameters, meta-information with user-driven semantics, and the job scripts. As distinguishing features, SUSHI provides an expert command line interface as well as a convenient web interface to run bioinformatics tools. SUSHI datasets are self-contained and self-documented on the file system. This makes them fully reproducible and ready to be shared. With the associated meta-information being formatted as plain text tables, the datasets can be readily further analyzed and interpreted outside SUSHI.
conclusionSUSHI provides an exquisite recipe for analysing NGS data. By following the SUSHI recipe, SUSHI makes data analysis straightforward and takes care of documentation and administration tasks. Thus, the user can fully dedicate his time to the analysis itself. SUSHI is suitable for use by bioinformaticians as well as life science researchers. It is targeted for, but by no means constrained to, NGS data analysis. Our SUSHI instance is in productive use and has served as data analysis interface for more than 1000 data analysis projects. SUSHI source code as well as a demo server are freely available.
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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.