SuperDecode is an integrated toolkit for analyzing mutations induced by genome editing. The toolkit provides three useful modules, including DSDecodeMS, HiDecode, and LaDecode, each tailored to automatically decode mutations from Sanger, high-throughput short-read, and long-read sequencing data of target-site amplicons, respectively.

How to obtain the standalone package?

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You can download the standalone version corresponding your computer system:

• Windows version: SuperDecode_win.zip

• Linux version: SuperDecode_linux.tar.gz

• MacOS version: SuperDecode_macOS.tar.gz

The standalone software has also beed desposited in Github. You can also download the latest version from this site (https://github.com/xiexr/SuperDecode)

After you download the binary file, please unzip it to your local disk (attention: ensure that no space or Chinese characters contained in the directory path).

How to use SuperDecode?

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We provide detailed expermental procedures and package usages for each module.

You can download the instruction document (in English or in Chinese) by clicking the below file.

• Instruction_of_SuperDecode_(in_English).pdf

• Instruction_of_SuperDecode_(in_Chinese).pdf

For large-scale samples (more than 30 or 50 samples), we recommend to use HiDecode or LaDecode for mutation analysis. In the document, we suggest a PCR-based strategy for constructing the NGS and TGS libraries. As described in the document, we suggest a set of sample barcodes for users. The suggested primers and barcode sequences can be download from here:

• Primers and barcodes for HiDecode: HiDecode_primers_and_barcodes.xlsx

• Primers and barcodes for LaDecode: LaDecode_primers_and_barcodes.xlsx

Note: Users can also define your own samples barcodes. Both the HiDecode and LaDecode programs allow users to reset the sample barcodes. In addition, the programs also support mutation analysis of sequencing data from simple targeted PCR amplicons of individual samples.