Jon Ambler attends ISMB/ECCB conference for computational biology
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.