Event:

Analysis pipelines for nanopore sequence data

Date: Tuesday 6th October 2020

Time: 3:00 pm (UK time)/ 10:00 am (EST)

Please join us for the next seminar in this series in which you will first hear from Anthony Doran, Technical Services Specialist, Oxford Nanopore Technologies Ltd., who will give an overview of the platform before we are joined by Julie Orjuela, IRD, and Pay Giesselmann, Max-Planck-Institute for Molecular Genetics, who will both present their analysis tools.

Participants of this webinar will learn about:

  • Oxford Nanopore data analysis workflows and research tools
  • Utilising pipelines to streamline and facilitate reproducible research
  • The application of snakemake as a platform for building analysis pipelines

There will also be an opportunity to submit questions throughout the talks which will be answered in the live Q&A session following the presentations.

Please register below to attend this webinar. You will receive a confirmation of your place from events@nanoporetech.com

Speaker details:

Anthony Doran, Technical Services Specialist, Oxford Nanopore Technologies

Anthony joined Oxford Nanopore Technologies in May 2019 as a Technical Services Specialist. He obtained his PhD from Maynooth University, Ireland, focusing on bioinformatics and systems biology approaches to investigate the functional basis of muscle growth in domesticated animal species. Following his PhD, he held joint positions as a senior bioinformatician at the Wellcome Trust Sanger Institute and the European Bioinformatics Institute, both based in Cambridge, UK. While in Cambridge, Anthony worked on creating de novo genome assemblies, and characterising whole genome variation primarily in humans and mouse models of human disease.  

Abstract

Data analysis pipelines are an integral aspect of bioinformatics that are frequently utilised in many analytical contexts. In this webinar, we will introduce what a data analysis pipeline is and highlight their importance in facilitating reproducible research. Using Oxford Nanopore Technologies’ research tools as an example, we will discuss the benefits of using a well-designed pipeline which uses established software, and represents analysis best practices.


Julie Orjuela, IRD

Julie Orjuela is a bioinformatic engineer at IRD and is interested in genomics and metagenomics, working mainly on plant domestication and crop pathogen interactions. Julie is a m ember of the multi - institute SouthGreen bioinformatics platform and is passionate about knowledge and technology transfer to southern countries.

Abstract

CulebrONT : a snakemake pipeline to benchmark Oxford Nanopore Technologies assemblies 

Long-reads from Oxford Nanopore Technologies could solve complex repeats and long structural variants. Assemblies are now more contiguous and accurate, but many tools are released every week and so it can be difficult to know which assembly tool could give the best results. W e have developed CulebrONT, a scalar, modulable and traceable snakemake pipeline that includes assembly, circularisation, polishing and correction steps, and has integrated the most relevant tools commonly used by Nanopore community. This workflow is an open source solution allowing to compare new assemblies (https://github.com/SouthGreenPlatform/CulebrONT_pipeline). CulebrONT has been used to benchmark prokaryotic and eukaryotic organisms.


Pay Giesselmann, Max-Planck-Institute for Molecular Genetics

Pay received his M.Eng. in Electrical Engineering from the Kiel University of Applied Sciences with a focus on embedded systems and hardware accelerated signal processing. He is currently a PhD student in Alex Meissner's lab at the Max-Planck-Institute for Molecular Genetics in Berlin. Pay is interested in the epigenetic regulation of the genome, direct base modification detection and developing tools and pipelines to process third generation sequencing data.

Abstract

Nanopype: a modular and scalable nanopore data processing pipeline

Oxford nanopore’s growing user base and continuously increasing throughput and accuracy are the driving forces behind development of countless bioinformatic tools for its data analysis. To facilitate rapid development and research, we developed Nanopype, which integrates the essentials of basecalling and alignment with a core set of downstream applications including methylation detection into a modular Snakemake pipeline. With automated builds and tests and deployment as Singularity containers, the package aims to provide reproducible production grade workflows for both workstation and cluster usage. Guaranteed standardized output formats make our pipeline an attractive framework no matter the subsequent analysis steps.

Availability: https://github.com/giesselmann/nanopype