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A Review of Scalable Bioinformatics Pipelines
10 references·3 citing·36 second hop
A Review of Scalable Bioinformatics Pipelines (2017)A Review of Scalable Bioinformatics Pipel…Toil enables reproducible, open source, big biomedical data analyses (2017)Toil enables reproducible, op…Nextflow enables reproducible computational workflows (2017)Nextflow enables reproducible…Use of application containers and workflows for genomic data analysis (2016)Use of application containers…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)The Galaxy platform for acces…RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS (2016)RABIX: AN OPEN-SOURCE WORKFLO…A review of bioinformatic pipeline frameworks (2016)A review of bioinformatic pip…Rethinking Data-Intensive Science Using Scalable Analytics Systems (2015)Rethinking Data-Intensive Sci…Dissemination of scientific software with Galaxy ToolShed (2014)Dissemination of scientific s…The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013)The Taverna workflow suite: d…Reproducible Research in Computational Science (2011)Reproducible Research in Comp…Trecode: A FAIR Eco-System for the Analysis and Archiving of Omics Data in a Combined Diagnostic and Research Setting (2022)Trecode: A FAIR Eco-System fo…Data Integration Strategies for Predictive Analytics in Precision Medicine (2018)Data Integration Strategies f…BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments (2018)BioWorkbench: a high-performa…Computational solutions to large-scale data management and analysis (2010)BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets (2016)PyGMQL: scalable data extraction and analysis for heterogeneous genomic datasets (2019)Design considerations for workflow management systems use in production genomics research and the clinic (2021)Taverna: a tool for building and running workflows of services (2006)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)AiiDA: automated interactive infrastructure and database for computational science (2015)BioContainers: an open-source and community-driven framework for software standardization (2017)Next-generation sequencing data interpretation: enhancing reproducibility and accessibility (2012)Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud (2015)Practical Computational Reproducibility in the Life Sciences (2017)Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)Snakemake—a scalable bioinformatics workflow engine (2012)snakePipes: facilitating flexible, scalable and integrative epigenomic analysis (2019)Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers (2021)Galaxy: A platform for interactive large-scale genome analysis (2005)What does research reproducibility mean? (2016)Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists (2010)Challenges of Big Data analysis (2014)An introduction to Docker for reproducible research (2015)Reproducible Bioconductor workflows using browser-based interactive notebooks and containers (2017)Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis (2017)Hot-starting software containers for STAR aligner (2018)Reproducibility: A tragedy of errors (2016)The nf-core framework for community-curated bioinformatics pipelines (2020)Sustainable data analysis with Snakemake (2021)The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024 (2024)Increasing value and reducing waste in research design, conduct, and analysis (2014)Reproducibility in Science (2014)Sustainable data analysis with Snakemake (2021)Methods included (2022)Building Containerized Workflows Using the BioDepot-Workflow-Builder (2019)uap: reproducible and robust HTS data analysis (2019)The role of metadata in reproducible computational research (2021)
this work references cited by second hop

References

  • 2017Nextflow enables reproducible computational workflows3,985 cited
  • 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update2,149 cited
  • 2011Reproducible Research in Computational Science1,446 cited
  • 2017Toil enables reproducible, open source, big biomedical data analyses1,362 cited
  • 2013The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud678 cited
  • 2014Dissemination of scientific software with Galaxy ToolShed257 cited
  • 2016A review of bioinformatic pipeline frameworks250 cited
  • 2015Rethinking Data-Intensive Science Using Scalable Analytics Systems96 cited
  • 2016Use of application containers and workflows for genomic data analysis35 cited
  • 2016RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS33 cited

Cited by

  • 2018Data Integration Strategies for Predictive Analytics in Precision Medicine16 cited
  • 2018BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments15 cited
  • 2022Trecode: A FAIR Eco-System for the Analysis and Archiving of Omics Data in a Combined Diagnostic and Research Setting11 cited

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