LAUSR

Motivation: Transposon insertion sequencing (Tn‐Seq) is a microbial systems‐level tool, that can determine on a genome‐wide scale and in high‐throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition. Results: Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non‐coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host‐factors that affect bacterial host susceptibility. MAGenTA is a complete Tn‐Seq analysis pipeline making sensitive genome‐wide fitness (i.e. growth rate) analysis available for most transposons and Tn‐Seq associated approaches (e.g. TraDis, HiTS, IN‐Seq) and includes fitness (growth rate) calculations, sliding window analysis, bottleneck calculations and corrections, statistics to compare experiments and strains and genome‐wide fitness visualization. Availability and implementation: MAGenTA is available at the Galaxy public ToolShed repository and all source code can be found and are freely available at https://vanopijnenlab.github.io/MAGenTA/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.