CRISPRessoSea: streamlined analysis and comparison of pooled amplicon CRISPR screens.

Samuel Coleman; Jacob Tye; Daxton Furniss; Robert Sainsbury; Abhay Rastogi; Xincen Xi; Balazs Murnyak; Jason Bell; Joseph Skeate; Minjing Wang; Beau Webber; Branden Moriarity; Kendell Clement

doi:10.1186/s12859-026-06518-9

PubMed · 42288725

CRISPRessoSea: streamlined analysis and comparison of pooled amplicon CRISPR screens.

Samuel Coleman·Jacob Tye·Daxton Furniss·Robert Sainsbury·Abhay Rastogi·Xincen Xi·Balazs Murnyak·Jason Bell·Joseph Skeate·Minjing Wang·Beau Webber·Branden Moriarity·Kendell Clement

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Abstract

BACKGROUND: CRISPR genome editing enables precise modification of genomic targets but may also induce unintended edits at off-target sites with similar sequences. Pooled amplicon sequencing can assess on- and off-target editing across many samples, yet analyzing, aggregating, and visualizing results from multiple pooled experiments remains challenging. Tools to simplify and standardize these analyses are needed to provide reproducible and comparable interpretation of editing data. RESULTS: We developed CRISPRessoSea, a software package that processes, compares, and visualizes genome editing rates from pooled amplicon sequencing experiments. The tool provides standardized workflows for analyzing editing across multiple targets and samples, supports both nuclease- and base-editing modalities, and generates clear, data-rich summaries suitable for downstream interpretation. CONCLUSIONS: CRISPRessoSea facilitates reproducible, scalable analysis of CRISPR editing outcomes across diverse experimental designs, enabling more efficient and transparent assessment of genome editing specificity. The software is freely available at https://github.com/clementlab/CRISPRessoSea .

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Software CRISPR-Cas Systems Gene Editing Clustered Regularly Interspaced Short Palindromic Repeats High-Throughput Nucleotide Sequencing CRISPR Genome editing Off-targets Pooled amplicon sequencing analysis Journal Article

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Samuel Coleman, Jacob Tye, Daxton Furniss, Robert Sainsbury, Abhay Rastogi, Xincen Xi, Balazs Murnyak, Jason Bell, Joseph Skeate, Minjing Wang, Beau Webber, Branden Moriarity, Kendell Clement. 2026-06-13. CRISPRessoSea: streamlined analysis and comparison of pooled amplicon CRISPR screens.. https://doi.org/10.1186/s12859-026-06518-9

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