SAW User Manual V8.0
  • Overview
  • Getting Started
    • Introduction
    • Glossary
  • Download Center
  • Analysis
    • Inputs
      • Chip mask
      • FASTQs
      • Images
    • Pipelines
      • SAW commands
      • count
        • Stereo-seq T FF
        • Stereo-seq N FFPE
    • Outputs
      • count outputs
      • realign outputs
      • HTML report
      • BAM
      • Matrices
      • Images
      • Analysis
  • Tutorials
    • Preparation of reference
    • Stereo-seq FF
    • Stereo-seq FFPE
    • With manually processed files
    • Secondary analysis
    • Format conversion
  • Algorithms
    • Read processing algorithms
    • Image processing algorithms
  • Advanced
    • Analysis with GPU
    • Expression matrix format
    • Image-related record format
  • Release Notes
  • SUPPORT PAGES
    • Datasets
    • Troubleshooting
    • Software and Kit Compatibility
    • Q & A
    • StereoMap
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On this page
  • System requirements
  • Software download
  • SAW 8.0.2 (July., 2024)
  • Compatibility
  • Reference download
  • Download & installation

Download Center

Last updated 6 months ago

To set up SAW in your computer environment, follow the steps below:

  • Check system requirements

  • Download SAW

  • Install SAW

  • Download references (optional)

System requirements

SAW pipelines on Linux systems that meet the following minimum requirements:

  • 8-core Intel or AMD processor (>24 cores recommended)

  • 128GB RAM (>256GB recommended)

  • 1TB free disk space or higher

  • 64-bit CentOS/RedHat 7.8 or Ubuntu 20.04

Software download

SAW 8.0.2 (July., 2024)

curl -o saw-8.0.2.tar.gz "https://enfile.stomics.tech/saw-8.0.2.tar.gz"
wget -O saw-8.0.2.tar.gz "https://enfile.stomics.tech/saw-8.0.2.tar.gz"

Compatibility

  • StereoMap >= v4.0 (compatibilty of history versions)

SAW 8.0 highlights

  • SAW is released as a self-contained tar.gz file that can be unpacked directly on the system, without the need to configure the computing environment.

  • Integrated and simplified pipelines facilitate inputting command lines and complete analysis. The pipelines include:

    • SAW count: the main pipeline to count gene expression reads and generate expression matrices from the Stereo-seq chip

      • SAW makeRef: prepare index files of the reference data

      • SAW checkGTF: check the annotation file format

      • SAW realign: restart analysis with manually processed files

      • SAW reanalyze: perform secondary analysis

      • SAW convert: support file format conversions

  • Gene expression from FFPE (formalin-fixed paraffin-embedded) samples is available in SAW, and is implemented by setting --kit-version to "Stereo-seq N FFPE V1.0", when running SAW count. SAW v8.0.0 or later is needed for FFPE analysis.

  • Microorganism analysis can be switched on when perform SAW count run based on Stereo-seq FFPE tissue sample, by using --microorganism-detect. You have to prepare indispensable references for it. More in Preparation of reference.

  • Upgraded the bioinformatical workflow of read alignment and annotation, which adapts to FFPE datasets.

    • During annotation, uniquely mapped reads and the best match among multi-mapped reads are used together by default. If the analyst focuses only on uniquely mapped reads, --uniquely-mapped-only will be helpful.

    • New spatial gene expression matrices are identified by unique gene ID, and record gene ID and name.

  • As for the image-related part, the software has optimized the image processing performance. Meanwhile, the microscope-stitched image, in TIFF, is supported as input directly when running SAW count.

  • Differential expression analysis is added to SAW analysis, which is performed based on Leiden clustering. Marker features are recorded both in AnnData H5AD and CSV, and displayed in HTML report and StereoMap.

  • The diagrams in the HTML report are interactive. The microorganism analysis page and the marker feature result table are added to the HTML report.

  • Reorganized output directory structure to make result files much clearer, and intermediate files and logs into designated folders.

  • Output the packaged visualization.tar.gz file, which includes .stereo file, containing SAW pipeline analysis information and records needed by StereoMap.

Release notes >

Reference download

SAW provides the reference data of mouse, jump to our datasets for downloads.

Download & installation

SAW is released as a self-contained tar.gz file that can be unpacked directly on the system, without the need to configure the computing environment. Because it has assembled all of the software-required dependencies, which are pre-compiled to run on most Linux distributions.

The reference and demo datasets need to be downloaded separately.

  • Step 1 - download the SAW software package and unpack it in a suitable location. Here sets /saw/package as the operation directory hypothetically.

$ cd /saw/package

[download the SAW package tar.gz from the Software download part]

$ tar -xzf saw-8.0.2.tar.gz

  • Step 2 - download the reference data and unpack it in a suitable location. Here sets /saw/reference as the operation directory hypothetically.

$ cd /saw/reference

[download the reference data from the Reference download part]

$ tar -xzf reference-data-mouse.tar.gz
# tar -xzf reference-data-mouse-rRNA.tar.gz

Access to help

Have any questions or concerns about downloads?

Please get in touch with the local agents or FAS/FBS.

Download for Linux 64-bit (tar.gz)

File size: 3.0 GB

md5sum: 0ca72ea8d7a990fdcf0ff88063ad2f77