Jon Ambler attends ISMB/ECCB conference for computational biology

23 Oct 2019 - 14:00

In July of 2019, Jon Ambler, CIDRI-Africa Bioinformatician, attended the ISMB/ECCB conference for computational biology in Basel, Switzerland. He presented work on a tool for the creation of genome graphs and met with a number of researchers working in the field. He was also able to obtain insight into current trends in high-throughput sequencing and general bioinformatics tools. The work presented has since been accepted for publication, and the project has seen an uptick in interest thanks to the exposure during this time.

Poster presentation:

  • The work presented during the poster session was received well, with a large number of people showing interest in the novel methods used.
  • A number of researchers working on genome graphs also offered to contribute to the project and integrate their methods into the GenGraph toolkit.
  • Looking at the web traffic for the GenGraph page during that time, a number of people also visited and downloaded the tool.
  • The full paper on GenGraph has since been accepted for publication in BMC bioinformatics.
  • View the poster at https://doi.org/10.7490/f1000research.1117242.1

 

Trends identified:

  • The use of nf-core as a way to package workflows and promote reusability and reproducibility has become widely accepted as common practice.
    • This is a collection of curated and well documented pipelines for bioinformatics analysis.
    • CIDRI-Africa should continue our work supporting the use of these pipelines and encourage researchers to move their workflows to NextFlow.
  • Genome graphs were at the centre of the high-throughput sequencing track
    • While everyone agreed that they are an essential development, many of the groups are struggling with challenges in runtime, file size, and accuracy.
  • Development of algorithms for synthetic long read clouds
    • This is a technique from 2016 that would drastically increase the ability to assemble genomes from short reads.
    • While the technique is sound, the tools for taking advantage of this technology still need work
    • This is intersecting with graph based assembly methods

Jon is looking forward to new collaborations fostered by his time in Switzerland, and implementing some of the methods and tools discussed at the conference.

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