SMRT Link
SMRT Link software tools for PacBio HiFi sequencing systems are designed to set up and monitor sequencing runs, review performance metrics, analyze, visualize, and annotate sequencing data. SMRT Link is available for both local installation and cloud access, offering flexibility to work in different environments depending on your lab’s needs.
SMRT Link
A web-based end-to-end workflow manager
- Supports all software needs for PacBio HiFi sequencing systems, from sample setup to analysis, using a single interface
- Provides fast, easy, and powerful analysis of SMRT sequencing data across a wide range of applications
- Free to use for PacBio customers – download SMRT Link from the HiFi software downloads page or contact tech support to access SMRT Link Cloud.
View SMRT Link application brief
SMRT Link features
SMRT Link software is available for both local installation and cloud access. See the installation guide for the requirements of each install.
| SMRT Link | SMRT Link Cloud | SMRT Link Lite | |
|---|---|---|---|
| Supported instruments | Revio, Vega, and Sequel IIe | Revio and Vega | Revio, Vega, and Sequel IIe |
| Sample setup | ✓ | ✓ | ✓ |
| Run design | ✓ | ✓ | ✓ |
| Run monitoring | ✓ | ✓ | ✓ |
| Instrument monitoring | ✓ | ✓ | ✓ |
| Push-button secondary analysis (SMRT Analysis) | ✓ | X | X |
| 3rd party and PacBio Compatible Partners analysis | ✓ | ✓ | ✓ |
| API access | ✓ | X | ✓ |
Sample setup
Calculate binding and annealing reactions for preparing DNA libraries for use on all PacBio HiFi sequencing systems.
Runs
View information about sequencing runs, monitor run progress, and create run designs.
Instruments
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.
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:
- HiFi mapping
- HiFi target enrichment
- Iso-Seq analysis
- Microbial genome analysis
- Read segmentation and Iso-seq
- Read segmentation and single-cell Iso-Seq
- Single-cell Iso-Seq
- Variant calling
- Read segmentation
- Demultiplexing
SMRT Link API
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.