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

---

Software download

SAW 8.0.2 (July., 2024)

Download for Linux 64-bit (tar.gz)

File size: 3.0 GB

md5sum: 0ca72ea8d7a990fdcf0ff88063ad2f77

curl

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

wget

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. 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

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

curl

#mouse
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-mouse.tar.gz" ./

#mouse with rRNA
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/refer
ence-data-mouse-rRNA.tar.gz" ./

#rat
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-rat.tar.gz" ./

#human
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-human.tar.gz" ./

#human with rRNA
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-human-rRNA.tar.gz" ./

wget

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

curl

#mouse for bowtie2
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-mouse-rRNA-Bowtie2.tar.gz" ./

#human for bowtie2
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-human-rRNA-Bowtie2.tar.gz" ./

wget

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

curl

#kraken2 database
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/reference-data-pluspf-20220908-Kraken2.tar.gz" ./

wget

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.

curl

#mouse
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/ProteinPanel_128_mouse_V2.list" ./

#human
curl -o aspera_download.key -s ftp://ftp.cngb.org/pub/Tool/Aspera/aspera_download.key && ascp -i aspera_download.key -P 33001 -T -k 1 -l 100m "aspera_download@183.239.175.39:/pub/stomics/STT0000124/supp/ProteinPanel_163_human_V2.list" ./

wget

---

Access to help

Have any questions or concerns about downloads?

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