UNLABELLED: We introduce IonGAP, a publicly available Web platform designed for the analysis of whole bacterial genomes using Ion Torrent sequence data. Besides assembly, it integrates a variety of comparative genomics, annotation and bacterial classification routines, based on the widely used FASTQ, BAM and SRA file formats. Benchmarking with different datasets evidenced that IonGAP is a fast, powerful and simple-to-use bioinformatics tool. By releasing this platform, we aim to translate low-cost bacterial genome analysis for microbiological prevention and control in healthcare, agroalimentary and pharmaceutical industry applications. AVAILABILITY AND IMPLEMENTATION: IonGAP is hosted by the ITER's Teide-HPC supercomputer and is freely available on the Web for non-commercial use at http://iongap.hpc.iter.es. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.