Why choose Nextflow as institution-wide bioinformatics workflow environment?

Dr Paul  Whatmore1, Assoc. Prof. Roberto  Barrero1, Mr Craig Windell1,2, Mr Chris Williams1, Prof. Matt Bellgard1

1eResearch Office, Queensland University of Technology, Brisbane, Australia
2QCIF, Brisbane, Australia

Bioinformatics enables and support life science research in the era of -omics technologies. Unsurprisingly, over the years there have been a variety of analytic workflow environments available that attempt to deliver end-to-end data analysis. However, studies are diverse and  invariably require continual workflow customisations.

When providing an institution-wide bioinformatics workflow capability, consideration must be given to the available computational infrastructure, workflow environments, analysis tools, level of researcher expertise (e.g., use of command-line), nature of the analysis. It is also important to adopt international harmonised analytical solutions to reduce duplication and maximise impact of findings.

As part of the bioinformatics workflow ecosystem, our eResearch Office has deployed the NextFlow environment and work in partnership with research groups, to implement customised workflow solutions. NextFlow is an open source workflow engine that supports many HPC and cloud engines. With a fluent Domain Specific Language and support for Containers, reproducibility and scalability is supported. There is an active global community that regularly publishes analysis pipelines. Researchers do not require significant overhead to use these pipelines beyond minimal command-line tool training, making it possible for new students to process large volume of data in a timely manner. Importantly, the pipelines can be easily modified and automatically provisioned for researchers.

This presentation provides an overview of the key features of NextFlow for a range of sophisticated analysis such as gene expression, variant calling and annotation, microbiome, normalised chromosome conformation capture contact maps, diagnostics of plant viruses/viroids, consensus genome calling.


Biography:

For the past 10 years Dr Whatmore has worked as a bioinformatician in Norway (Institute of Marine Research) and Australia (GU, USC, QUT). He has been with QUT since March 2020, developing bioinformatic analysis pipelines and supporting research staff and HDR students, as well as teaching courses on R. He has supported research projects involving a variety of species, including model (mice, human, zebrafish) and various non-model organisms, which included a variety of ‘omics’ technologies and data types, such as DNA methylation, circular RNAs, variant calling, genome assembly, metagenomics and gene expression.

Date

Oct 14 2021
Expired!

Time

2:40 pm - 3:00 pm

Local Time

  • Timezone: America/New_York
  • Date: Oct 13 - 14 2021
  • Time: 11:40 pm - 12:00 am