Reducing Costs by Up to 87% Using AWS Batch with Seqera

By Amazon Web Services

December 11, 2023

Biotech software company Seqera wanted to unlock scale for high performance computing (HPC) while maintaining ease of use for scientists worldwide. Scientists, engineers, and developers download Seqera’s open-source software, Nextflow, more than 160,000 times each month to power their bioinformatics workloads. But with datasets reaching petabytes in size, Seqera was challenged to provide researchers with the compute resources they need.

The company built its solutions on Amazon Web Services (AWS) to stay focused on creating customer value. “AWS was the logical cloud to build on, given our requirements for performance, scale, flexibility, and global reach,” says Evan Floden, CEO and cofounder at Seqera. “Our decision to build on AWS has been backed by our customers, most of whom build on AWS as well.”

Opportunity | Using AWS Batch to Deliver HPC to Global Customers for Seqera

In the life sciences, researchers are hard at work predicting potential pandemics, developing lifesaving therapeutics, and studying complex biological systems. In 2013, a team of scientists in Barcelona led by Paolo Di Tommaso, chief technology officer and cofounder at Seqera, created Nextflow—an open-source project to accelerate the pace of discovery through bioinformatics. Although the team used to operate its own HPC data centers, it soon found that because bioinformatics operations have sudden bursts of use followed by periods of less activity, these workloads are well suited for the cloud. The organization started using AWS services in the mid-2010s, and Nextflow fully embraced AWS in 2017 after the release of AWS Batch—a service that empowers developers, scientists, and engineers to efficiently run hundreds of thousands of batch and machine learning computing jobs while optimizing compute resources.

In 2018, the Nextflow team formed Seqera to help users streamline their journeys into data collaboration at scale. In 2020, Seqera launched Seqera Platform (formerly Nextflow Tower), a centralized command post for Nextflow pipelines. “As our project and user base grew over time, we developed strong connections with the AWS team,” says Floden. “AWS support has been critical to the emergence of our open-source community.” By 2023, Seqera had more than 7,000 global members in its nf-core community, an independent effort to collect a curated set of high-quality pipelines built using Nextflow. Moreover, Seqera is now an AWS Partner serving people in more than 47 countries.

On AWS, we offer customers convenience, cost-effectiveness, and high throughput.”

Evan Floden
CEO and Cofounder, Seqera

Solution | Powering 6x Revenue Growth in 24 Months Using AWS Cloud Services

Seqera has seen an overwhelmingly positive response to the launch of Seqera Platform, which comes in two versions: one self-hosted, the other on the cloud. The company reports that the cloud solution, which was built on AWS, has grown by 160 percent to roughly 8,000 users in 18 months, during which time the corporate customer base has more than doubled. “We have increased revenue by six times over the past 24 months,” says Floden.

With its solutions on AWS, Seqera is meeting its goal of delivering cost-optimized HPC solutions to the scientific community. An estimated 20,000 scientists, engineers, and developers use Nextflow daily, and downloads have grown by 190 percent in 18 months. “On AWS, we offer customers convenience, cost-effectiveness, and high throughput,” says Floden.

Seqera reduced costs by implementing a resource optimization feature into Seqera Platform. “With the new Seqera resource optimization feature, we’ve demonstrated that production-scale pipelines on AWS can run up to 40 percent faster,” says Floden. “We’ve also dramatically reduced the cost of pipeline runs for our customers—up to 87 percent in some cases.”

Seqera customers have several options for deploying Seqera Platform…

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