Additional analysis with ConNIS

## Reproducibility note This repository contains a focused re-analysis of eight published Tn5-based TraDIS/Tn-Seq studies using the ConNIS method: - https://academic.oup.com/hr/article/12/9/uhaf160/8169913#528502292 - https://www.nature.com/articles/s41467-018-07379-4 - https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.01288/full - https://www.pnas.org/doi/10.1073/pnas.1220225110 - https://journals.asm.org/doi/10.1128/jb.00164-25 - https://www.sciencedirect.com/science/article/pii/S2211124723008586 - https://journals.asm.org/doi/10.1128/spectrum.02162-22 - https://journals.asm.org/doi/10.1128/jb.00771-15 For each study, the corresponding pipeline script in this repository documents the steps used to generate (i) an insertion-site list and (ii) a gene annotation table (gene/locus tag, start, stop) as input to ConNIS. Upstream processing from raw sequencing reads to insertion-site maps typically involves multiple bioinformatic steps (e.g., filtering/trimming, mapping, QC, counting) and may depend on study-specific choices (e.g., transposon construct, read structure, mapping parameters). Where the original publications did not provide a fully specified, ready-to-run pipeline (or the exact intermediate files), we implemented a best-effort reconstruction based on the Methods and supplementary information, aiming to match the described procedures as closely as possible. As a consequence, the exact insertion-site maps produced here may differ from the (potentially unpublished) internal processing used in the original studies. The goal of this repository is therefore to provide a transparent and reproducible re-analysis workflow and corresponding ConNIS results, rather than to claim bitwise identity with the original insertion-site calls.