Supplementary Code 1 & 2 Associated with the Article "Key Determinants of CRISPR/Cas9 Induced Inversions in Tomato"

This deposit includes the supplementary scripts used in the study "Key Determinants of CRISPR/Cas9 Induced Inversions in Tomato".

Supplementary Code 1 is an R script that runs the CRISPR/Cas9 software AmpliCan to analyze Hi-Seq .fq data. The script installs the necessary package, loads it, and executes the amplicanPipeline function with specified parameters to analyze the sequencing data. The sequencing data used for this analysis is available in the Sequence Read Archive (SRA) of NCBI under BioProject PRJNA1111086. For Supplementary Code 1, use the Excel file 'supplementary_code_1_config' as a config file template required for AmpliCan.

Supplementary Code 2 includes a script for searching inversion patterns at double-strand break (DSB) sites within PacBio FASTA files. Note that the PacBio .fq data should be converted to .fasta format to use Supplementary Code 2. The sequencing data generated during this study have been deposited in the Sequence Read Archive (SRA) of NCBI under BioProject PRJNA1111086. We used the AmpliCan R package as described in the article by Labun et al. (2019): Labun, K., Guo, X., Chavez, A., Church, G., Gagnon, J.A. and Valen, E. (2019) Accurate analysis of genuine CRISPR editing events with AmpliCan. Genome Research, 29, 843-847.