TIDE is a method for quantitatively assessing genome editing by sequence trace decomposition. It requires only two PCR reactions and two capillary sequencing runs to analyze the sequence traces and identify the major induced mutations in the editing site. The method is cost-effective and provides more detailed information than current enzyme-based assays. An interactive web tool is available for automated decomposition of sequence traces. TIDE facilitates the testing and rational design of genome editing strategies. Genome editing tools such as TAL effector nucleases, zinc finger nucleases, and RNA-guided endonucleases enable targeted mutagenesis. These methods introduce a DNA double-strand break (DSB), which is repaired by non-homologous end-joining, resulting in a mixture of unaltered and mutated DNA. The latter consists of short deletions and insertions around the break site. To determine the frequency of the desired editing event, PCR, cloning, and sequencing are used, but this is labor-intensive and costly. High-throughput sequencing is an alternative but expensive and time-consuming. TIDE uses two PCR reactions followed by capillary sequencing to analyze the sequence traces. The resulting traces are analyzed using a decomposition algorithm that identifies the major induced mutations and their frequencies. The algorithm aligns the sgRNA sequence to the control sequence to determine the expected break site. It then aligns the control sequence region upstream of the break site to the experimental sample sequence to determine any offset. The software uses peak heights to determine the relative abundance of aberrant nucleotides. The TIDE software first visualizes the proportion of aberrant base signals along the sequence traces. It then decomposes the composite sequence trace into individual components using multivariate non-negative linear modeling. This decomposition results in an estimate of the relative abundance of every possible indel within a chosen size range. The software provides an R² value as a goodness-of-fit measure and calculates the statistical significance for each indel. In vitro experiments showed that TIDE can accurately identify and quantify the constituent indels in a mixture. Application to CRISPR/Cas9 edited DNA sequences showed that TIDE can determine the efficiency of genome editing and the frequency of indels. The results were validated by cloning and sequencing individual DNA molecules. TIDE is highly robust and can detect insertions and deletions with a sensitivity up to ~1-2%. TIDE is a cost-effective and accurate method for assessing genome editing efficacy. It is applicable to various genome editing tools based on targeted DSB induction. It can also be used to study mechanisms of DSB repair and the effects of various indels on cellular fitness. TIDE is a valuable tool for a broad diversity of research involving genome editing methods.TIDE is a method for quantitatively assessing genome editing by sequence trace decomposition. It requires only two PCR reactions and two capillary sequencing runs to analyze the sequence traces and identify the major induced mutations in the editing site. The method is cost-effective and provides more detailed information than current enzyme-based assays. An interactive web tool is available for automated decomposition of sequence traces. TIDE facilitates the testing and rational design of genome editing strategies. Genome editing tools such as TAL effector nucleases, zinc finger nucleases, and RNA-guided endonucleases enable targeted mutagenesis. These methods introduce a DNA double-strand break (DSB), which is repaired by non-homologous end-joining, resulting in a mixture of unaltered and mutated DNA. The latter consists of short deletions and insertions around the break site. To determine the frequency of the desired editing event, PCR, cloning, and sequencing are used, but this is labor-intensive and costly. High-throughput sequencing is an alternative but expensive and time-consuming. TIDE uses two PCR reactions followed by capillary sequencing to analyze the sequence traces. The resulting traces are analyzed using a decomposition algorithm that identifies the major induced mutations and their frequencies. The algorithm aligns the sgRNA sequence to the control sequence to determine the expected break site. It then aligns the control sequence region upstream of the break site to the experimental sample sequence to determine any offset. The software uses peak heights to determine the relative abundance of aberrant nucleotides. The TIDE software first visualizes the proportion of aberrant base signals along the sequence traces. It then decomposes the composite sequence trace into individual components using multivariate non-negative linear modeling. This decomposition results in an estimate of the relative abundance of every possible indel within a chosen size range. The software provides an R² value as a goodness-of-fit measure and calculates the statistical significance for each indel. In vitro experiments showed that TIDE can accurately identify and quantify the constituent indels in a mixture. Application to CRISPR/Cas9 edited DNA sequences showed that TIDE can determine the efficiency of genome editing and the frequency of indels. The results were validated by cloning and sequencing individual DNA molecules. TIDE is highly robust and can detect insertions and deletions with a sensitivity up to ~1-2%. TIDE is a cost-effective and accurate method for assessing genome editing efficacy. It is applicable to various genome editing tools based on targeted DSB induction. It can also be used to study mechanisms of DSB repair and the effects of various indels on cellular fitness. TIDE is a valuable tool for a broad diversity of research involving genome editing methods.