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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  • Release Notes for SAW
  • 8.0.2 (July., 2024)
  • 8.0.1 (July., 2024)
  • 8.0.0 (June., 2024)
  • Previous ones

Release Notes

Release Notes for SAW

8.0.2 (July., 2024)

Bug fixes:

  • Fixed several known issues.

8.0.1 (July., 2024)

Bug fixes:

  • Fixed several known issues.

8.0.0 (June., 2024)

New Form:

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.

New Feature:

  • 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.

Previous ones

Release information for earlier versions can also be found on our GitHub.

Access to help

Have any questions or concerns about SAW versions?

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

Last updated 6 months ago