NextflowSeqera

Deploying GPU Accelerated Nextflow Pipelines on Nebius Kubernetes with Seqera

This is a companion post to our protein design pipeline blog post. While the previous post covers the science and the pipeline itself, this one walks through the infrastructure side: how we set up Nebius AI Cloud to run GPU-accelerated Nextflow workflows at production scale using managed Kubernetes and Seqera.

Florian Wuennemann
Daria Balashova
Florian Wuennemann & Daria Balashova
Mar 25, 2026
Seqera

SSH into Your Studio Session: Work the Way You Want, Where Your Data Resides

Seqera Studios now supports direct SSH access to running Studio sessions. This means you can connect to a live, cloud-based Studio container using any standard SSH client — or better yet, use VS Code’s Remote - SSH extension to work inside the remote session as if it were your local machine.

Rob NewmanRob Newman
Mar 18, 2026
NextflowSeqera

Introducing the Seqera AI CLI - Your AI-Powered Terminal Assistant for Nextflow Development

Today we introduce the Seqera AI CLI – an intelligent command-line assistant that brings context-aware AI directly to your Nextflow development. This powerful tool transforms how you build, run, and manage Nextflow pipelines, all from the comfort of your terminal.

Sasha DagayevSasha Dagayev
Mar 03, 2026
Seqera

50% Faster Delivery, 4x Faster Pipeline Development: Transforming Bioinformatics Operations

Here, we showcase how a life sciences bioinformatics core recently transformed their operations with Nextflow and Seqera, to achieve a 50% improvement in data delivery time and 4x faster pipeline development.

Lizzie BolithoLizzie Bolitho
Feb 11, 2026
Seqera

Streamlined Version Control for Studios: Introducing Git Repository Integration

At the recent Nextflow Summit, we announced a powerful new capability for Seqera Studios: native Git repository integration. This update transforms how teams manage interactive analysis environments by bringing version control directly into the Studio creation workflow, enabling reproducible, shareable, and team-friendly development environments.

Rob NewmanRob Newman
Jan 15, 2026
Seqera

Building a Scalable Protein Design Pipeline with Seqera AI for Adaptyv's Nipah Binder Competition

Here, we demonstrate how we used Seqera AI to build a scalable protein design pipeline that helped us rank 6th (based on ipSAE ranking) in Adaptyv’s Nipah Binder Competition

Florian Wuennemann
Edmund Miller
Florian Wuennemann & Edmund Miller
Jan 08, 2026
Seqera

End-to-End AI-Enabled Variant Analysis in Seqera Studios with the Help of AIVA

Studios enables researchers to perform AIVA's AI-powered variant analysis – enabling seamless integration between bioinformatics pipelines and clinical analysis.

Drew DiPalma
Tarun Mamidi
Drew DiPalma & Tarun Mamidi
Dec 11, 2025
NextflowSeqera

Bioinformatics Pipelines Through the Ages: From Bash to Nextflow to Agents

Bioinformatics tools and workflows are rapidly transforming to address increasing complexity and demands for reproducibility, scalability, and collaboration. Here's my retrospective on this evolution in the industry.

Ken BrewerKen Brewer
Dec 10, 2025
Seqera

Simplifying Workflow Automation: Node-RED Integration for Seqera

We’re delighted to announce that we’ve just released a new Node-RED integration for Seqera which democratizes automation, enabling researchers to build workflows without depending on IT teams.

Phil EwelsPhil Ewels
Nov 25, 2025
Seqera

What’s New at Seqera: GxP-Aligned Bioinformatics, Expanded Data Connections, AI Integrations, and More

I began today's Nextflow Summit talking about our vision to make scientists' lives simpler, one pipeline at a time. The same platform, but better suited to bioinformatics in 2025. Every product update we’ve announced today builds on this foundation, moving us through the complete journey from scientific infrastructure, through innovation and velocity. From GxP-aligned pipeline versioning and in-platform data exploration on HPC, to AI in Platform and our new MCP Server, here’s the latest Seqera updates you won’t want to miss.

Evan FlodenEvan Floden
Oct 23, 2025
CommunitySeqera

Enabling Single-Cell Benchmarks at Scale: The OpenProblems.bio, Viash, and Seqera Partnership

Single-cell analysis sits at the intersection of machine learning and biology. Advances in microfluidic technology have transformed data collection, creating large, tabular datasets well suited to machine-learning (ML) methods. OpenProblems.bio formalizes evaluating approaches into living, community‑run benchmarks (curated tasks, datasets, methods, and metrics) and then executes them as robust pipelines.

Evan Floden
Robrecht Cannoodt
Evan Floden & Robrecht Cannoodt
Oct 14, 2025
Seqera

Introducing the Seqera MCP Server: Bringing Seqera to Your Preferred AI Agent

The AI revolution is reshaping how we interact with computational infrastructure. We recently announced the Seqera AI Integration in Platform, our purpose-built bioinformatics AI that can directly execute, debug, and launch workflows within Seqera Platform. Today, we're taking the next decisive step forward by opening Seqera to the entire AI ecosystem through our new Seqera MCP server. Fully integrated with Seqera single sign on (SSO), you can make your preferred AI tool (e.g. Claude AI, VS Code Copilot, Cursor) your new control center for Seqera Platform.

Paolo Di TommasoPaolo Di Tommaso
Oct 09, 2025
Seqera

Achieve Granular Cloud Resource Tracking with Dynamic Resource Labels

Today, we are excited to announce dynamic resource labels — a new Seqera Platform feature that solves the per-workflow cost tracking challenge by automatically injecting unique workflow and session identifiers into every cloud job. This removes the necessity for manual configuration, whether your workflows run in AWS, Azure, or Google Cloud.

Anton Tsyganov-Bodounov
Llewellyn van der Berg
Anton Tsyganov-Bodounov & Llewellyn van der Berg
Oct 07, 2025
Seqera

6 Reasons Why Bioinformatics is Hard and How Seqera Helps

As science accelerated, teams needed more than just workflow tools, they needed better data integration, scalability, and collaboration. Scientific progress was getting stuck because the technology was too complex. That’s why we created Nextflow and Seqera. In the blog post, we highlight six core problems that make bioinformatics harder than it should be and how Seqera, the Nextflow-first tech stack, addresses each one.

Esha JoshiEsha Joshi
Sep 18, 2025
Seqera

Seqera AI in Platform: Develop, Debug, and Execute in One Unified Experience

Today, we're excited to announce that Seqera AI now has read and write access to Seqera Platform. This enables Seqera AI to directly interact with Seqera Platform primitives to debug pipelines, modify parameters, and launch runs, all without switching context between different tools and interfaces.

Sasha DagayevSasha Dagayev
Sep 16, 2025
Seqera

What’s New: Seqera Platform Enterprise Release 25.2

Seqera Platform Enterprise 25.2 delivers significant enhancements across security, observability, and flexibility to accelerate your workflow orchestration capabilities. Key updates in this release include redesigned user interfaces, expanded cloud support, and powerful new development tools.

Drew DiPalmaDrew DiPalma
Sep 04, 2025
Seqera

Optimizing High-Throughput Bioinformatics with Fusion

Fusion is the cloud-native file system designed and optimized for Nextflow pipelines that removes these barriers. It simplifies infrastructure, enhances performance, and cuts costs, making it easier for bioinformaticians to develop, maintain, and scale pipeline code.

Paolo Di TommasoPaolo Di Tommaso
Aug 19, 2025
Seqera

Scaling with Seqera: From Prototype to Enterprise-Grade Deployment

Modern scientific research doesn’t just scale up, it scales in every direction: across code, compute, teams, and projects. Today, success isn’t measured by how much data is processed, but by how rapidly teams can adapt, reproduce results, and scale efficiently. Seqera exists to enable this. In this blog, we explore how the Seqera ecosystem empowers R&D leaders to scale innovation, streamline operations, and deliver faster, more reproducible scientific outcomes.

Esha JoshiEsha Joshi
Aug 14, 2025
Seqera

Accelerating Innovation: Inside the Genomics England Hackathon 2025

Last month, Seqera hosted a hackathon with Genomics England, bringing together bioinformaticians and Nextflow experts to tackle real-world challenges and enhance workflow capabilities. Over 2 days, teams tackled several critical projects, from following nf-core best practices to converting legacy WDL variant calling pipelines to Nextflow. The goal was to accelerate development, build technical confidence, and embed best practices across Genomics England.

Rike Hanssen
Adam Talbot
Harshil Patel
Rike Hanssen, Adam Talbot & Harshil Patel
Aug 06, 2025
Seqera

Replatforming Science: Software as a Strategic Lever in Modern Pharma R&D

The pharmaceutical industry stands at a pivotal moment. Organizations now find themselves constrained, not by the science, but by the software and systems supporting it. Here, I’ll outline five major shifts redefining how biopharma teams are scaling their research operations, and why these changes are shaping scientific performance, collaboration, and long-term agility.

Evan FlodenEvan Floden
Jul 01, 2025
Seqera

Seqera AI: Pipeline Mode, SRA Search, GitHub Integration, and the Nextflow VS Code Extension

We’ve introduced powerful new enhancements to Seqera AI that elevate how you build, understand, and optimize Nextflow pipelines. Whether you’re starting from scratch or refining complex workflows, Seqera AI delivers deeper insight and smarter automation at every step of the development lifecycle. In this blog post, we highlight what’s new with Seqera AI.

Sasha DagayevSasha Dagayev
Jun 26, 2025
Seqera

BigOmics Meets Studios: End-to-end Exploration of RNA-Seq and Proteomics Data in Seqera Platform

BigOmics Analytics have partnered with Seqera to bring Omics Playground (BigOmics’ interactive RNA-seq and proteomics workbench) into Studios (the interactive analysis feature of Seqera Platform). The result is a seamless, end-to-end path from raw reads to interactive plots, all deployed on the same infrastructure as your Nextflow pipelines.

Rob Syme
Axel Martinelli
Rob Syme & Axel Martinelli
Jun 25, 2025
Seqera

Seqera Integrates NVIDIA Parabricks and Fusion to Seamlessly Accelerate Genomics Analysis

NVIDIA and Seqera have partnered to combine the strengths of NVIDIA® Parabricks®,a GPU-accelerated software suite for omics, and Fusion, Seqera’s optimized filesystem for cloud-native Nextflow pipelines. Together, these technologies dramatically accelerate data analysis, reduce costs, and simplify cloud infrastructure for bioinformatics teams.

Edmund Miller
Rike Hanssen
Rob Syme
Florian Wuennemann
Edmund Miller, Rike Hanssen, Rob Syme & Florian Wuennemann
Jun 12, 2025
Seqera

Deploying custom applications in Seqera Studios

Studios already provides pre-built, version-controlled container template images (namely Jupyter, R IDE, VS Code, and Xpra). But what if you need an application we don’t offer? The solution: add your own. In this blog post, we’ll demonstrate how to build custom Docker images for Studios and highlight useful examples.

Edmund Miller
Florian Wuennemann
Jon Manning
Edmund Miller, Florian Wuennemann & Jon Manning
May 28, 2025
Seqera

What’s New from Seqera: Product Highlights from the Nextflow Summit

At Nextflow Summit Boston 2025, we unveiled a series of exciting product updates to do just that. From compute optimization and pipeline resilience, to smarter platform intelligence and an elevated developer experience, here are the key product highlights you won’t want to miss.

Drew DiPalmaDrew DiPalma
May 16, 2025
Seqera

Seqera Compute - Managed, Optimized Compute for Scalable Bioinformatics

Today, we’re thrilled to announce the Public Preview of Seqera Compute — fully managed, optimized compute for scientists to run Nextflow pipelines and interactive analyses effortlessly. Built for scalability and security, Seqera Compute ensures a hassle-free Nextflow and interactive analysis experience, empowering teams to move faster, scale smarter, and do more — all without the infrastructure burden.

Evan FlodenEvan Floden
May 15, 2025
Seqera

Discovery Demands Infrastructure: Why Research Can’t Scale Without It

We’re at a tipping point in how research infrastructure must evolve. Too often we encounter world-class teams who are spending their time configuring compute environments, debugging pipelines, or stitching together incompatible tooling. That’s not innovation, it’s inefficiency disguised as necessity.

Evan FlodenEvan Floden
May 08, 2025
Seqera

Scaling the Future of Scientific Software: Seqera Raises $26M Series B

Today, we're ecstatic to announce that Seqera has raised $26 million in Series B funding, led by Addition with participation from Speedinvest, Talis, Amino Collective, BoxOne, and SNR. This milestone marks a bold step forward in our mission to build the world’s most indispensable software-first platform for bioinformatics and life science R&D.

Evan FlodenEvan Floden
May 06, 2025
Seqera

Seqera Achieves SOC 2 Type II Attestation

We’re excited to share that Seqera is now SOC 2 Type II attested—a significant milestone in our ongoing commitment to security, trust, and compliance.

Arnau Alcázar LleopartArnau Alcázar Lleopart
Apr 17, 2025
Seqera

Seqera Studios is now generally available: Interactive analysis starts here

We are excited to announce that Studios, a powerful feature of Seqera Platform that enables interactive analysis with fully customizable containers and compute environments, is now generally available. Explore how Studios is accelerating the entire data lifecycle and get a sneak peek at exciting new and upcoming features.

Rob NewmanRob Newman
Apr 09, 2025
NextflowSeqera

Bringing Seqera AI to the Nextflow VS Code extension

We are excited to announce a powerful new GitHub Copilot integration within the Nextflow VS Code extension. Workflow development has never been faster or more intuitive.

Sasha DagayevSasha Dagayev
Apr 08, 2025
Seqera

How utilizing resource labels on Seqera can help with high resolution cost analysis in AWS

This blog post provides a step-by-step guide to setting up and understanding resource labels within Seqera Platform and how they can be used to tag AWS infrastructure resources for detailed cost reporting across your workflows and teams.

Florian WuennemannFlorian Wuennemann
Mar 11, 2025
Seqera

Shifting Paradigms: Considerations for the Scientific Data Lifecycle

Today, sequencing and imaging is faster, cheaper, and more accessible than ever. Research is no longer constrained by what we can sequence, but by what we can meaningfully deduce, forcing a paradigm shift in how we approach computation, storage, and interpretation.

Evan FlodenEvan Floden
Feb 27, 2025
Seqera

Running Nextflow Workflows with Seqera and Slurm on Nebius AI Cloud Platform

Explore how to leverage Seqera Platform and Slurm on Nebius AI Cloud platform using Soperator (Slurm operator for Kubernetes) to deploy scalable Nextflow workflows.

Florian Wuennemann
Alexander Kim
Florian Wuennemann & Alexander Kim
Feb 19, 2025
Seqera

Automating resource creation with Seqerakit

By addressing the growing need for automation, Seqerakit helps scientists reclaim their time from repetitive tasks and focus on extracting meaningful insights from their genomic data.

Llewellyn van der BergLlewellyn van der Berg
Jan 31, 2025
Seqera

From legacy scripts to ready-to-run Nextflow pipelines with Seqera AI

Bioinformaticians often develop unique, in-house workflows using common workflow languages —such as Bash, Python, and R—choosing the one that best aligns with their project requirements, datasets, and computational resources.

Sasha DagayevSasha Dagayev
Jan 08, 2025
Seqera

Running AI workloads on Seqera: Maximizing computational resources with mixed GPU and CPU environments

Discover how Seqera Platform’s Batch Forge simplifies the process of creating versatile hybrid compute environments, letting you harness the power of both CPU and GPU instances on the cloud, all optimized for Nextflow workflows.

Rike Hanssen
Rob Syme
Rike Hanssen & Rob Syme
Dec 23, 2024
Seqera

5 Product Announcements You Won’t Want to Miss from Nextflow Summit Barcelona

At the Nextflow Summit in Barcelona last month, we announced some exciting product updates to further our mission to advance science for everyone through software. Here are five key product announcements from the Nextflow Summit that you won’t want to miss!

Elizabeth BolithoElizabeth Bolitho
Nov 19, 2024
Seqera

Step-by-Step Series: Protein structure prediction in Seqera

Last month, the developers of AlphaFold2 were awarded the 2024 Nobel Prize in Chemistry. Did you know you can easily perform 3D protein structure prediction analysis using AlphaFold2 and other AI models in Seqera?

Llewellyn van der BergLlewellyn van der Berg
Nov 01, 2024
Seqera

Empowering scientific discovery through AI innovation

At Seqera, we believe that AI isn’t just a tool - it’s the future of scientific discovery. We're committed to harnessing its transformative power to revolutionize the Life Sciences.

Evan FlodenEvan Floden
Oct 24, 2024
Seqera

Step-by-Step Series: RNA-Seq analysis in Seqera

We are excited to launch our new Step-by-Step blog series on running Nextflow pipelines in Seqera Platform. With accompanying technical guides, the series also demonstrates how to create and configure environments for flexible tertiary analysis and troubleshooting with Studios.

Llewellyn van der BergLlewellyn van der Berg
Oct 11, 2024
Seqera

Bioinformatics events you can’t miss in fall 2024 and early 2025

Get ready to mark your calendars because the fall of 2024 is going to be jam-packed with amazing opportunities to expand your knowledge, make new connections, and stay at the forefront of bioinformatics!

Irina SilvaIrina Silva
Sep 24, 2024
AnnouncementSeqera

Seqera acquires tinybio to Advance Science for Everyone - Now Through GenAI!

We are thrilled to announce that Seqera is joining forces with tinybio, a NYC-based tech-bio start-up known for its AI-integrated scientific tools focused on executing pipelines and analyses via natural language.

Evan FlodenEvan Floden
Aug 06, 2024
SeqeraAnnouncement

Seqera's project on the optimization of computational resources for HPC workloads in the cloud through ML/AI has been funded by the European Union

Call for grants 2021 aimed at R&D Projects in AI and other digital technologies and their integration into value chains

Teresa VillosladaTeresa Villoslada
Jun 05, 2024
Seqera

Empowering scientists with seamless access to bioinformatics resources

Today marks a major milestone in that journey as we release two new free and open resources for the community: Seqera Pipelines and Seqera Containers.

Evan FlodenEvan Floden
May 23, 2024
NextflowSeqeranf-core

nf-core/riboseq: A collaboration between Altos Labs and Seqera

This is a joint article contributed to the Seqera blog by Jon Manning of Seqera and Felix Krueger of Altos Labs describing the new nf-core/riboseq pipeline.

Jon ManningJon Manning
May 15, 2024
SeqeraNextflow

7 tips for reducing your Nextflow cloud spend

An updated look at best practices for managing cloud spending with Nextflow and the Seqera platform.

Evan FlodenEvan Floden
Apr 30, 2024
SeqeraNextflow

Singularity Reloaded

Improved Singularity/Apptainer support in Nextflow and Wave.

Marco De La Pierre
Marco De La Pierre
Apr 18, 2024
Seqera

Element Biosciences and Seqera – Flexible, powerful, end-to-end analysis at scale

Automating NGS data analysis in the cloud ElemBio cloud and Seqera

Harshil PatelHarshil Patel
Apr 05, 2024
Seqera

Fusion file system and Mountpoint for Amazon S3 – understanding the differences

When processing bioinformatics datasets, having the right file system is essential. Read our in-depth article and learn why the Fusion file system is uniquely suited to large-scale analysis.

Jordi Deu PonsJordi Deu Pons
Feb 27, 2024
Seqera

Seqera at ASHG 2023

Seqera presents a poster on large-scale data analysis pipelines.

Noel OrtizNoel Ortiz
Nov 14, 2023
Seqera

Seqera and AWS Fargate

Reduce startup times for Nextflow pipelines.

Gord SissonsGord Sissons
Oct 30, 2023
Seqera

Introducing Data Explorer

Simplified data management for Nextflow pipelines.

Drew DiPalmaDrew DiPalma
Oct 18, 2023