AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines [version 1; peer review: awaiting peer review]

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics da...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:F1000 research Jg. 13; S. 1257
Hauptverfasser: Oh, Sehyun, Gravel-Pucillo, Kai, Ramos, Marcel, Schatz, Michael C., Davis, Sean, Carey, Vincent, Morgan, Martin, Waldron, Levi
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England F1000 Research Limited 2024
F1000 Research Ltd
Schlagworte:
AnVIL
Cloud Computing
Computational Biology - methods
eng
Genomics
Genomics - methods
Humans
R/Bioconductor
Software
Software Tool
Workflow
Workflows
Cloud computing
R/Bioconductor
AnVIL
Workflows
Genomics
ISSN:2046-1402, 2046-1402
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung:Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. We present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflow simplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflow for three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. AnVILWorkflow lowers the barrier to utilizing AnVIL's resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project ( https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub ( https://github.com/shbrief/AnVILWorkflow).
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.155449.1