CHOPCHOP v3 is an updated web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. This version expands the tool's functionality beyond genome editing to include targeting RNA with Cas13, supporting alternative transcript isoforms and RNA accessibility predictions. It also incorporates new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. The results page visualization has been expanded to reveal alternative isoforms and downstream ATG sites, helping users avoid truncated protein expression. CHOPCHOP v3 now supports over 200 genomes and includes a command-line script for running larger jobs and handling unsupported genomes. The tool now supports CRISPR–Cas13 targeting, which involves searching for off-targets across the complete transcriptome rather than the genome. RNA accessibility is calculated using RNAfold from the Vienna RNA package. The tool also supports various CRISPR–Cas targeting modes, including nanopore enrichment, knock-in, and activation/repression. The new version includes predictions of DSB repair outcomes, efficiency scores for Cas12a/Cpf1, and updated efficiency scores for Cas9. CHOPCHOP v3 also allows users to target the entire gene, not just specific isoforms, and includes three transcriptomes for RNA knockdown (human, mouse, and zebrafish). The tool is now available as a command-line version, compatible with ampliCan for sequencing-based mutation assessment. The update reflects the expanding CRISPR toolbox and accommodates the needs of over 200 research groups. The CHOPCHOP server is available at https://chopchop.cbu.uib.no; the Python code for local installation is available at https://bitbucket.org/valenlab/chopchop.CHOPCHOP v3 is an updated web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. This version expands the tool's functionality beyond genome editing to include targeting RNA with Cas13, supporting alternative transcript isoforms and RNA accessibility predictions. It also incorporates new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. The results page visualization has been expanded to reveal alternative isoforms and downstream ATG sites, helping users avoid truncated protein expression. CHOPCHOP v3 now supports over 200 genomes and includes a command-line script for running larger jobs and handling unsupported genomes. The tool now supports CRISPR–Cas13 targeting, which involves searching for off-targets across the complete transcriptome rather than the genome. RNA accessibility is calculated using RNAfold from the Vienna RNA package. The tool also supports various CRISPR–Cas targeting modes, including nanopore enrichment, knock-in, and activation/repression. The new version includes predictions of DSB repair outcomes, efficiency scores for Cas12a/Cpf1, and updated efficiency scores for Cas9. CHOPCHOP v3 also allows users to target the entire gene, not just specific isoforms, and includes three transcriptomes for RNA knockdown (human, mouse, and zebrafish). The tool is now available as a command-line version, compatible with ampliCan for sequencing-based mutation assessment. The update reflects the expanding CRISPR toolbox and accommodates the needs of over 200 research groups. The CHOPCHOP server is available at https://chopchop.cbu.uib.no; the Python code for local installation is available at https://bitbucket.org/valenlab/chopchop.