Curtin University Homepage
  • Library
  • Help
    • Admin

    espace - Curtin’s institutional repository

    JavaScript is disabled for your browser. Some features of this site may not work without it.
    View Item 
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item

    eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity

    Access Status
    Fulltext not available
    Authors
    Mousaviderazmahalleh, Mahsa Mousavi
    Stott, Audrey
    Lines, Rose
    Peverley, Georgia
    Nester, Georgia
    Simpson, Tiffany
    Zawierta, Michal
    De La Pierre, Marco
    Bunce, Michael
    Christophersen, Claus
    Date
    2021
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Mousavi-Derazmahalleh, M. and Stott, A. and Lines, R. and Peverley, G. and Nester, G. and Simpson, T. and Zawierta, M. et al. 2021. eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity. Molecular Ecology Resources. 21 (5): pp. 1697-1704.
    Source Title
    Molecular Ecology Resources
    DOI
    10.1111/1755-0998.13356
    ISSN
    1755-098X
    Faculty
    Faculty of Science and Engineering
    School
    School of Molecular and Life Sciences (MLS)
    School of Elec Eng, Comp and Math Sci (EECMS)
    URI
    http://hdl.handle.net/20.500.11937/86511
    Collection
    • Curtin Research Publications
    Abstract

    Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way biodiversity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state-of-the-art applications to process eDNA data from raw sequences (single-end or paired-end) to generation of curated and noncurated zero-radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high-performance computing (HPC) clusters. Finally, we present an in-house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an example of a published coral diversity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 samples. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data; scalability and reproducibility.

    Related items

    Showing items related by title, author, creator and subject.

    • From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
      Murray, D.; Coghlan, Megan; Bunce, Michael (2015)
      Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by ...
    • The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north-western Australia
      West, Katrina M.; Adam, Arne A.S. ; White, Nicole ; Robbins, William ; Barrow, D.; Lane, A.; Richards, Zoe (2022)
      The application of environmental DNA technologies is a promising new approach to rapidly audit biodiversity across large-scale, remote regions. Here, we examine the efficacy of a dual-assay eDNA metabarcoding approach for ...
    • Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea
      DiBattista, J.; Coker, D.; Sinclair-Taylor, T.; Stat, M.; Berumen, M.; Bunce, Michael (2017)
      Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral ...
    Advanced search

    Browse

    Communities & CollectionsIssue DateAuthorTitleSubjectDocument TypeThis CollectionIssue DateAuthorTitleSubjectDocument Type

    My Account

    Admin

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Follow Curtin

    • 
    • 
    • 
    • 
    • 

    CRICOS Provider Code: 00301JABN: 99 143 842 569TEQSA: PRV12158

    Copyright | Disclaimer | Privacy statement | Accessibility

    Curtin would like to pay respect to the Aboriginal and Torres Strait Islander members of our community by acknowledging the traditional owners of the land on which the Perth campus is located, the Whadjuk people of the Nyungar Nation; and on our Kalgoorlie campus, the Wongutha people of the North-Eastern Goldfields.