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Ewels P, Krueger F, Käller M, et al. Cluster Flow: A user-friendly bioinformatics workflow tool. F1000Res. 2016;5:2824doi: 10.12688/f1000research.10335.2.
Ewels, P., Krueger, F., Käller, M., & Andrews, S. (2016). Cluster Flow: A user-friendly bioinformatics workflow tool. F1000Research, 52824. https://doi.org/10.12688/f1000research.10335.2
Ewels, Philip, et al. "Cluster Flow: A user-friendly bioinformatics workflow tool." F1000Research vol. 5 (2016): 2824. doi: https://doi.org/10.12688/f1000research.10335.2
Ewels P, Krueger F, Käller M, Andrews S. Cluster Flow: A user-friendly bioinformatics workflow tool. F1000Res. 2016 Dec 06;5:2824. doi: 10.12688/f1000research.10335.2. eCollection 2016. PMID: 28299179; PMCID: PMC5310375.
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F1000Res. 2016 Dec 06;5:2824. doi: 10.12688/f1000research.10335.2. eCollection 2016.

Cluster Flow: A user-friendly bioinformatics workflow tool.

F1000Research

Philip Ewels, Felix Krueger, Max Käller, Simon Andrews

Affiliations

  1. Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
  2. Bioinformatics Group, The Babraham Institute, Cambridge, UK.
  3. Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden.

PMID: 28299179 PMCID: PMC5310375 DOI: 10.12688/f1000research.10335.2

Abstract

Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.

Keywords: Bioinformatics; Data analysis; Next-generation sequencing; Parallel computing; Pipeline; Workflow

Conflict of interest statement

Competing interests: No competing interests were disclosed.

References

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  2. Bioinformatics. 2012 Oct 1;28(19):2520-2 - PubMed
  3. Bioinformatics. 2016 Oct 1;32(19):3047-8 - PubMed
  4. Nat Biotechnol. 2017 Apr 11;35(4):316-319 - PubMed

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