Developmental Biology
Nature
Cells
Plant Physiology
Stem Cell Research
The CRISPR Journal
GENE
Genomics
BMC Plant Biology
Frontiers in Endocrinology
Frontiers in Molecular Biosciences
Molecular Therapy
American Journal of Physiology
DECODR is used for analysis and cited in top
publications
Our foundational paper in The CRISPR Journal established the DECODR software platform as a powerhouse of Sanger sequencing-based genome editing analysis
Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data
Bloh K, Kanchana R, Bialk P, et al. The CRISPR Journal, 2021
During CRISPR-directed gene editing, multiple gene repair mechanisms interact to produce a wide and largely unpredictable variety of sequence changes across an edited population of cells. Shortcomings inherent to previously available proposal-based insertion and deletion (indel) analysis software necessitated the development of a more comprehensive tool that could detect a larger range and variety of indels while maintaining the ease of use of tools currently available.
To that end, we developed Deconvolution of Complex DNA Repair (DECODR). DECODR can detect indels formed from single or multi-guide CRISPR experiments without a limit on indel size. The software is accurate in determining the identities and positions of inserted and deleted bases in DNA extracts from both clonally expanded and bulk cell populations. The accurate identification and output of any potential indel allows for DECODR analysis to be executed in experiments utilizing potentially any configuration of donor DNA sequences, CRISPR-Cas, and endogenous DNA repair pathways.
“DECODR utilizes a unique proposal generation and determination algorithm that allows accurate uncovering of indel identities, including those of inserted bases. This greater accuracy of genetic content determination allows users to be better informed about the exact genetic changes their CRISPR edits are creating."
“Moreover, DECODR is particularly valuable when indel sequence information is necessary for clonal cell analysis, as it has the unique capability to predict inserted sequences …”
"Among the four tools [TIDE, ICE, DECODR and SeqScreener], DECODR provided the most accurate estimations of indel frequencies...DECODR was found to be the most useful when one wishes to identify indel sequences."
Systematic Comparison of Computational Tools for Sanger Sequencing-Based Genome Editing Analysis
Aoki et al. Cells, 2024
“Linear regression analysis showed that DECODR analysis corresponded significantly with NGS analysis compared to TIDE- or Synthego [ICE] - reported indels..."
"...this analysis highlights the utility of DECODR for indel analysis of in vivo, somatic CRISPR models in comparison to TIDE and Synthego [ICE].”
Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models
Brockman et al. Science Reports, 2023
"...the DECODR tool enables accurate, quantitative assessment of multi-allelic indels from a single Sanger trace, out-performing other tools such as TIDE, ICE, Cas-analyzer, HI-TOM, and CRISP-ID by detecting a broader range of indel types and sizes."
Recent publications utilizing DECODR software: