Genome editing using CRISPR/Cas(clustered regularly interspaced short palindromic repeats/CRISPRassociated protein)or other systems has become a cornerstone of numerous biological and applied research fields.However,d...Genome editing using CRISPR/Cas(clustered regularly interspaced short palindromic repeats/CRISPRassociated protein)or other systems has become a cornerstone of numerous biological and applied research fields.However,detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient.In response to this issue,we designed SuperDecode,an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies.SuperDecode comprises threemodules,DSDecodeMS,HiDecode,and LaDecode,each designed to automatically decode mutations from Sanger,high-throughput short-read,and long-read sequencing data,respectively,from targeted PCR amplicons.By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons,HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex targetsite editing in a cost-effective manner.We demonstrate the efficacy of SuperDecode by analyzingmutations produced using different genome editing tools(CRISPR/Cas,base editing,and prime editing)in differentmaterials(diploid and tetraploid rice and protoplasts),underscoring its versatility in decoding genome editing outcomes across different applications.Furthermore,this toolkit can be used to analyze other genetic variations,as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene.SuperDecode offers both a standalone software package and a web-based version,ensuring its easy access and broad compatibility across diverse computer systems.Thus,SuperDecode provides a comprehensive platformfor analyzing a wide array ofmutations,advancing the utility of genomeediting for scientific research and genetic engineering.展开更多
The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical...The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical limitations persist in current computational tools for quantifying editing efficiency-particularly concerning data processing capabilities,analytical throughput,and operational flexibility.This research presents SuperDecode,a novel computational framework designed to address these methodological constraints.The SuperDecode offers key advantages,including local processing capabilities,large-size sequencing files,batch-processing,and diversified operational functions.展开更多
基金supported by the Biological Breeding-National Major Project(2023ZD04074)Invigorate the Seed Industry of Guangdong Province(2023-NJS-00-012).
文摘Genome editing using CRISPR/Cas(clustered regularly interspaced short palindromic repeats/CRISPRassociated protein)or other systems has become a cornerstone of numerous biological and applied research fields.However,detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient.In response to this issue,we designed SuperDecode,an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies.SuperDecode comprises threemodules,DSDecodeMS,HiDecode,and LaDecode,each designed to automatically decode mutations from Sanger,high-throughput short-read,and long-read sequencing data,respectively,from targeted PCR amplicons.By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons,HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex targetsite editing in a cost-effective manner.We demonstrate the efficacy of SuperDecode by analyzingmutations produced using different genome editing tools(CRISPR/Cas,base editing,and prime editing)in differentmaterials(diploid and tetraploid rice and protoplasts),underscoring its versatility in decoding genome editing outcomes across different applications.Furthermore,this toolkit can be used to analyze other genetic variations,as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene.SuperDecode offers both a standalone software package and a web-based version,ensuring its easy access and broad compatibility across diverse computer systems.Thus,SuperDecode provides a comprehensive platformfor analyzing a wide array ofmutations,advancing the utility of genomeediting for scientific research and genetic engineering.
文摘The CRISPR-Cas system has revolutionized modern life sciences,enabling groundbreaking applications ranging from functional genomics to therapeutic development.Despite its transformative potential,significant technical limitations persist in current computational tools for quantifying editing efficiency-particularly concerning data processing capabilities,analytical throughput,and operational flexibility.This research presents SuperDecode,a novel computational framework designed to address these methodological constraints.The SuperDecode offers key advantages,including local processing capabilities,large-size sequencing files,batch-processing,and diversified operational functions.
