Software tools for Sequel II/IIe and Revio systems designed to set up and monitor long-read HiFi sequencing runs, review performance metrics, analyze, visualize, and annotate sequencing data.

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A web-based end-to-end workflow manager

  • Supports all software needs within the Sequel II/IIe and Revio systems, from sample setup to analysis results, using a single interface
  • Provides fast, easy, and powerful analysis of SMRT sequencing data across a wide range of applications
  • Free to download — visit the HiFi software downloads page to download SMRT Link


Sample setup

Calculate binding and annealing reactions for preparing DNA libraries for use on all Revio, Sequel II and Sequel IIe systems.



View information about sequencing runs, monitor run progress, and create run designs.

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View information about instruments connected to SMRT Link, including sequencing status, remaining run time, and pre-load availability for the next run.


Data management

Create projects and data sets; generate QC reports for data sets; view, import, or delete sequence, reference, and barcode files.

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SMRT analysis

Perform secondary analysis on the basecalled data, including sequence alignment, variant detection, structural variant calling, and RNA analysis.

SMRT analysis software

SMRT Analysis in SMRT Link includes a comprehensive set of applications for push-button analyses, such as de novo assembly, variant identification, RNA analysis, and more. The applications included are:

  • Genome assembly
  • HiFi mapping
  • HiFi target enrichment
  • HiFiViral SARS-Cov-2 analysis
  • Iso-Seq analysis
  • Microbial genome analysis
  • Read segmentation and Iso-seq
  • Read segmentation and single-cell Iso-Seq
  • Single-cell Iso-Seq
  • Structural variant calling
  • Variant calling
  • Read segmentation
  • Demultiplexing

Learn more

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Use the SMRT Link API to integrate with LIMS and other applications, automatically set up runs, pull custom run metrics, poll for when jobs are complete so you can trigger a new job to run, and more.

The SMRT Link API is now easier than ever to use with easy Python examples for almost any use case.


Download API Python reference

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SMRT Link vs SMRT Link Lite

SMRT Link Lite contains all features of SMRT Link except SMRT Analysis. See the installation guide for information about compute needed to run SMRT Link Lite.

SMRT Link SMRT Link Lite
Sample setup
Run design
Run monitoring
Instrument monitoring
Push-button secondary analysis (SMRT analysis) X


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