Download Center

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

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Software download

SAW 8.1.3 (Mar., 2025)

Download for Linux 64-bit (tar.gz)

File size: 5.7 GB

md5sum: 6cd872cffcf539a8c3a2e5447bc290cd

curl

curl -o saw-8.1.3.tar.gz "https://enfile.stomics.tech/saw-8.1.3.tar.gz"

wget

Compatibility

• StereoMap >= v4.0 (compatibility with history versions)

SAW-8.1 highlights

• Stereo-CITE FF samples is available in SAW released as a self-contained tar.gz file. It is implemented by setting --kit-version to "Stereo-CITE T FF V1.x", when running SAW count. SAW v8.1.0 or later is needed for Stereo-CITE FF analysis.

• Supported Stereo-seq FF kit=V1.3 by setting --kit-version to "Stereo-seq T FF V1.3"when running SAW count.

• SAW reanalyze is called by submodules, and you can use functions like:

  • SAW reanalyze lasso

  New functions:

  • SAW reanalyze midFilter Performe manually filtering spatial expression matrices by MID range.

  • SAW reanalyze multiomics Proteome & Transcriptome joint analysis.

  • SAW reanalyze removeBackground Automatic protein background removal.

• Upgraded the bioinformatical workflow

  • Defaultly cutting adapters in SAW count alignment, instead of directly discarding reads with adapter.

  • Clustering in bin GEF mode omits zero-centering variables to handle sparse input.

  • Adjusted marker selection thresholds in Proteome & Transcriptome joint analysis.

• The compressed image .tar.gz file completed by feature point registration from StereoMap, can be accpeted by --image-tar. SAW v8.1.0 or later is needed for feature point registration.

• Fixed the appearance of cells with large single area after cell segmentation. Improve tissue segmentation based on image.

• Reduce memory usage in SAW count Annotation.

• SAW count and realign output HTML report as <SN>.report.html , and you can open it directly. Page Square Bin can display bin20 and bin50 clustering and UMAP projection.

Release notes >

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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. 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-8.1.3.tar.gz

Reference download

STOmics R&D has pre-built reference genome index files that can be used directly.

Index files for STAR alignment

Index File	Description	File Information
​reference-data-mouse.tar.gz​	Mouse reference for STAR alignment, including genome file, annotation file and index files.	File size: 27.84GB md5sum: 67c79da93b3575b31c7a97fe6e2f17f0
​reference-data-mouse-rRNA.tar.gz​	Mouse reference with rRNA information for STAR alignment, including genome file, annotation file and index files.	File size: 28.03GB md5sum: 6fa47b14dc26321d1cab691baee4fb2f
​reference-data-rat.tar.gz​	Rat reference for STAR alignment, including genome file, annotation file and index files.	File size: 27.55GB md5sum: 92dc19ab97b5ad1a16f3f1dfd34cd642
​reference-data-human.tar.gz​	Human reference for STAR alignment, including genome file, annotation file and index files.	File size: 31.20GB md5sum: 881b966dcd3e253cdf5ef5c36ec588dc
​reference-data-human-rRNA.tar.gz​	Human reference with rRNA information for STAR alignment, including genome file, annotation file and index files.	File size: 31.47GB md5sum: a86ceda324fa300d18f48b77502e5274

wget

#mouse
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-mouse.tar.gz

#mouse with rRNA
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-mouse-rRNA.tar.gz

#rat
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-rat.tar.gz

#human
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-human.tar.gz

#human with rRNA
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-human-rRNA.tar.gz

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 mouse referencetar.gz from the reference download part]

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

Index files for Bowtie2 alignment

Index File	Description	File Information
​reference-data-mouse-rRNA-Bowtie2.tar.gz​	Mouse reference with rRNA information for Bowtie2 alignment, including genome file and index files.	File size: 3.89GB md5sum: 2c8dd1293390009ba2a10cb28d757a74
​reference-data-human-rRNA-Bowtie2.tar.gz​	Human reference with rRNA information for Bowtie2 alignment, including genome file and index files.	File size: 4.32GB md5sum: 3fcc26c8df319706634514e8e5b17d73

wget

#mouse for bowtie2
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-mouse-rRNA-Bowtie2.tar.gz

#human for bowtie2
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-human-rRNA-Bowtie2.tar.gz

Taxonomy reference for Kraken2 alignment

Index File	Description	File Information
​reference-data-pluspf-20220908-Kraken2.tar.gz​	Taxonomy reference for Kraken2 alignment.	File size: 48.47GB md5sum: 46e56a6d2707066758574d203579d1d9

wget

wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/reference-data-pluspf-20220908-Kraken2.tar.gz

Protein panels for PID mapping

Species	Protein panel	MD5	Cocktail information
mouse	​ProteinPanel_128_mouse_V2.list​	8745033762db89d5a4096232e54e6521	TotalSeq-A™ Mouse Universal Cocktail, V1.0 (Cat. No. 199901)
human	​ProteinPanel_163_human_V2.list​	64a20baa464ba38aa1f7f93286b18bed	TotalSeq-A™ Human Universal Cocktail, V1.0 (Cat. No. 399907)

*Know more details according to Cocktail information.

wget

#mouse
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/ProteinPanel_128_mouse_V2.list

#human
wget -c ftp://ftp2.cngb.org/pub/stomics/STT0000124/supp/ProteinPanel_163_human_V2.list

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Access to help

Have any questions or concerns about downloads?

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