Cassette_gatherer_hunter

This repository contains all sequencing data and reference files generated in the study “Large-scale recovery of integron cassettes for gene discovery screens”. The dataset includes raw long-read sequencing reads (FASTQ), processed mapping files (BAM), reference genome sequences used for alignment (FASTA), and annotated genes and integron cassette coordinates (CSV). We have also included the results generated with the adapted FeatureCounts script used to analyze these libraries. Custom R scripts are described in the GitHub Repository: https://github.com/mredrejo/cassette_gatherer_hunter. These files enable full reproduction of the cassette mapping analyses and representation quantification described in the manuscript.