Interrogation of double-strand break repair mediated by CRISPR genome editing using CRISPAltRations

CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair footprints that result from non-homologous end joining after double stranded breaks were introduced by Cas9 or Cas12a for more than 500 paired treatment/control experiments. We found that building our understanding into a novel analysis tool improved results quality. We validated our software using simulated rhAmpSeq amplicon sequencing data and demonstrate that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR associated indels and homology directed repair events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user-interface and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a UI we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.