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.
DSDecodeMS
It identifies mutations (heterozygous or biallelic mutations) directly from Sanger sequencing chromatograms of target-site-containing PCR amplicons.
DSDecode is suggested used for decoding mutations for diploid organisms.
HiDecode
It identifies small mutations (including chimeric and mosaic mutations) from large numbers of samples (diploid or polyploid organisms, cell lines,
protoplasts or calli) by analyzing short-read next-generation sequencing (NGS) data.
LaDecode
It identifies complex mutations, induced by multiplexed editing within a certain region using long-read
third-generation sequencing (TGS). For complex structural variations, LaDecode is highly suggested.
SuperDecode not only enables the web-based analysis, but also provide standalone package for users that can be easily used in different computer systems.
For HiDecode and LaDecode module, we highly suggest you to download the standalone version and analyze your data on your local computer.
How to obtain the standalone package?
The standalone software has also beed desposited in Github. You can 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?
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
Contact us
If you have any suggestions or problems in using SuperDecode, please feel free to contact us.
You can contact us by E-mail (xiexianrong@scau.edu.cn) or through TBtools community.
Statement
SuperDecode is freely available to non-commercial users. For commercial using, please contact us.