Scale without the premium. Introducing VITARI™ 
Contact Us

      ElemBio™ Cloud API and CLI

      Build, automate, and analyze on our sequencing and multiomics platforms

      Explore everything you need to work programmatically with AVITI™, AVITI24™, and VITARI™ data, using ElemBio Cloud API and CLI, and surrounded by a full ecosystem of open analysis tools.

      elembio cloud api and cli

      ElemBio Cloud API: A REST API for your runs and metrics

      A REST API that surfaces the same run data you see in ElemBio Cloud and is ready to power dashboards, monitoring tools, LIMS read-back, and custom automation in any language.

      What you can do

      • List and filter runs by status, type, instrument, or date
      • Retrieve run details, and QC metrics
      • Track analysis flow execution status
      • Download run files and analysis outputs on demand
      • Mount run data as a read-only local directory without downloading files
      • Feed run data into your LIMS or data warehouse

      How it works

      With an ElemBio Catalyst™ subscription, your run data is available in ElemBio Cloud, accessible through the ElemBio API or CLI, and ready to power custom automation pipelines and natural-language AI agents.

      Developer_Resources_Page_Fig1 (1)

      The ElemBio Cloud API and CLI use standard REST conventions, bearer-token auth, JSON responses, and predictable HTTP status codes.

      Resources

      The API exposes a small set of core resources, each addressable over standard REST endpoints:


      RESOURCE

      DESCRIPTION

      Runs

      Sequencing run records you can list and filter by status, type, instrument, or date.

      Run details

      Full run metadata and quality metrics for an individual run.

      Analysis flows

      Execution status and outputs of the analysis flows tied to your runs.

      Instruments

      Your instruments and their status across the fleet.

      Files

      Run files and analysis outputs to download on demand or mount as a read-only directory.

      Use cases

      Put the REST API to work on automating pipelines, feeding dashboards and warehouses, and powering natural-language AI agents.


      AUTOMATION & PIPELINES

      • Detect run completion and pull metrics automatically.

      • Retrieve FASTQ and analysis files to kick off your downstream analysis.

      DATA INTEGRATION & DASHBOARDS

      • Sync run metadata and results into your LIMS, warehouse, or dashboards.

      • Push to an internal data lake on a schedule.

      AI AGENTS & NATURAL LANGUAGE

      • Let AI agents query your runs, instruments, and metrics.

      • Summarize results and analyze trends.

       

      REST API Getting Started Guide

      ElemBio Cloud CLI: A scriptable shell for the API

      A single binary CLI that wraps the API in human-friendly commands. You can drop it into cron jobs, CI pipelines, Nextflow workflows, or use it for quick fleet checks.

      Key features

      ONE BINARY, ZERO DEPENDENCIES

      Install once on macOS, Linux, or Windows with no dependencies to manage.

      SECURE, SCOPED LOGIN

      Authenticate once with a scoped API token and your credentials stay safely stored.

      FULL FLEET VISIBILITY

      List and inspect runs, executions, and instruments across your whole lab.

      BUILT FOR AUTOMATION

      Drop commands into cron, CI, or Nextflow without writing HTTP client code.

      MOUNT RUN DATA (FUSE)

      Stream cloud files as a read-only local directory without downloads.

       

      Use cases

      SCRIPTING & CI

      • Run quick commands in bash, cron, or CI pipelines.

      • Script repetitive tasks across many runs.

      BULK & REMOTE ACCESS

      • Download large run outputs from any terminal.

      • Skip writing HTTP client code for routine pulls.

      EASY DATA SHARING

      • Share run and execution data with a single command.

       

       

      CLI Getting Started Guide

      Open tools and tutorials

      The wider ecosystem extends downstream of the API and CLI, starting with ElemBio Catalyst, our cloud compute and storage platform that provides secure, region-specific compute and data management and optimized bioinformatic workflows, including:

      Bases2Fastq

      Convert base calls into FASTQ files locally for any downstream bioinformatics pipeline.

      Documentation →

      Cells2Stats

      Cells2Stats processes multiomics data to generate detailed statistics and outputs that enable downstream analysis and visualization.

      Documentation →

      Python notebooks

      Python notebooks for resegmenting cells and clustering multiomics data with to visualize cell populations in a UMAP.

      Documentation →

      Seurat integration

      Integrate AVITI24 data with Seurat to unlock the wider single-cell analysis ecosystem.

      Documentation →

      Cloud service providers

      Connect providers such as AWS, DNAnexus, Google Cloud, and Seqera for storage connections, compute activities, and verified flows.

      Documentation →

       

       

      Learn more about ElemBio Catalyst

      Designed with intent, built for your discovery

      Our instruments