Articlegold2018

Closha: bioinformatics workflow system for the analysis of massive sequencing data

Gunhwan Ko · Pan-Gyu Kim · Jongcheol Yoon · Gukhee Han · Seong‐Jin Park · Wangho Song +1 more

27 citations0/0 files storedBMC Bioinformatics

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Scientific Computing and Data Management Genomics and Phylogenetic Studies Genetics, Bioinformatics, and Biomedical Research

Abstract

BACKGROUND: While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines. The integration of data and analytic resources into workflow systems provides a solution to the problem by simplifying the task of data analysis. RESULTS: To address this challenge, we developed a cloud-based workflow management system, Closha, to provide fast and cost-effective analysis of massive genomic data. We implemented complex workflows making optimal use of high-performance computing clusters. Closha allows users to create multi-step analyses using drag and drop functionality and to modify the parameters of pipeline tools. Users can also import the Galaxy pipelines into Closha. Closha is a hybrid system that enables users to use both analysis programs providing traditional tools and MapReduce-based big data analysis programs simultaneously in a single pipeline. Thus, the execution of analytics algorithms can be parallelized, speeding up the whole process. We also developed a high-speed data transmission solution, KoDS, to transmit a large amount of data at a fast rate. KoDS has a file transfer speed of up to 10 times that of normal FTP and HTTP. The computer hardware for Closha is 660 CPU cores and 800 TB of disk storage, enabling 500 jobs to run at the same time. CONCLUSIONS: Closha is a scalable, cost-effective, and publicly available web service for large-scale genomic data analysis. Closha supports the reliable and highly scalable execution of sequencing analysis workflows in a fully automated manner. Closha provides a user-friendly interface to all genomic scientists to try to derive accurate results from NGS platform data. The Closha cloud server is freely available for use from http://closha.kobic.re.kr/ .

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References

2010Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences 2016The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 2004Taverna: a tool for the composition and enactment of bioinformatics workflows 2012Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

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2022A Survey of Biological Data in a Big Data Perspective 2019Bioinformatics Workflows With NoSQL Database in Cloud Computing 2022Trecode: A FAIR Eco-System for the Analysis and Archiving of Omics Data in a Combined Diagnostic and Research Setting

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