A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads

Authors

  • Gihan Gamage University of Moratuwa
  • Indika Perera University of Moratuwa
  • Dulani Meedeniya University of Moratuwa https://orcid.org/0000-0002-4520-3819
  • Anuradha Welivita École polytechnique fédérale de Lausanne

DOI:

https://doi.org/10.3991/ijoe.v16i08.14821

Keywords:

Genome assembly, Gamification, Human Computing Games, Next Generation Sequencing

Abstract


Next-generation sequencing has revolutionized the field of genomics by producing accurate, rapid and cost-effective genome analysis with the use of high throughput sequencing technologies. This has intensified the need for accurate and performance efficient genome assemblers to assemble a large set of short reads produced by next-generation sequencing technology. Genome assembly is an NP-hard problem that is computationally challenging. Therefore, the current methods that rely on heuristic and approximation algorithms to assemble genomes prevent them from arriving at the most accurate solution. This paper presents a novel approach by gamifying whole-genome shotgun assembly from next-generation sequencing data; we present "Geno", a human-computing game designed with the aim of improving the accuracy of whole-genome shotgun assembly. We evaluate the feasibility of crowdsourcing the problem of whole-genome shotgun assembly by breaking the problem into small subtasks. The evaluation results, for single-cell Escherichia coli K-12 substr. MG1655 with a read length of 25 bp that produced 144,867 game instances of mean 25 sequences per instance at 40x coverage indicate the feasibility of sub-tasking the problem of genome assembly to be solved using crowdsourcing.

Author Biography

Dulani Meedeniya, University of Moratuwa

Dr. D. Meedeniya is a Senior Lecturer in the Department of Computer Science and Engineering, at the University of Moratuwa, Sri Lanka. She holds a PhD in Computer Science from the University of St Andrews, United Kingdom. Her main research interests are Software modelling and design, Workflow tool support for bioinformatics, Data Visualization and Recommender systems. She is a Fellow of HEA(UK), MIET, MIEEE and a Charted Engineer registered at EC (UK).

Downloads

Published

2020-07-17

How to Cite

Gamage, G., Perera, I., Meedeniya, D., & Welivita, A. (2020). A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads. International Journal of Online and Biomedical Engineering (iJOE), 16(08), pp. 68–84. https://doi.org/10.3991/ijoe.v16i08.14821

Issue

Vol. 16 No. 08 (2020)

Section

Papers

License

The submitting author warrants that the submission is original and that she/he is the author of the submission together with the named co-authors; to the extend the submission incorporates text passages, figures, data or other material from the work of others, the submitting author has obtained any necessary permission.
Articles in this journal are published under the Creative Commons Attribution Licence (CC-BY What does this mean?). This is to get more legal certainty about what readers can do with published articles, and thus a wider dissemination and archiving, which in turn makes publishing with this journal more valuable for you, the authors.
By submitting an article the author grants to this journal the non-exclusive right to publish it. The author retains the copyright and the publishing rights for his article without any restrictions.