Serverless Nanopore Basecalling with AWS Lambda

The serverless computing paradigm allows simplifying operations, offers highly parallel execution and high scalability without the need for manual management of underlying infrastructure. This paper aims to evaluate if recent advancements such as container support and increased computing resource limits in AWS Lambda allow it to serve as an underlying platform for running bioinformatics workflows such as basecalling of nanopore reads. For the purposes of the paper, we developed a sample workflow, where we focused on Guppy basecaller, which was tested in multiple scenarios. The results of the experiments showed that AWS Lambda is a viable platform for basecalling, which can support basecalling nanopore reads from multiple sequencing reads at the same time while keeping low infrastructure maintenance overhead. We also believe that recent improvements to AWS Lambda make it an interesting choice for a growing number of bioinformatics applications.