title: IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.
abstract: 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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  mcolesan@ull.edu.es or cflores@ull.edu.es
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Information Technology Department, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
authors.forename: Adrian
authors.initials: A
authors.lastname: Baez-Ortega
authors.affiliation: Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.
authors.forename: Fabian
authors.initials: F
authors.lastname: Lorenzo-Diaz
authors.affiliation: Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
authors.forename: Mariano
authors.initials: M
authors.lastname: Hernandez
authors.affiliation: Information Technology Department, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
authors.forename: Carlos Ignacio
authors.initials: CI
authors.lastname: Gonzalez-Vila
authors.affiliation: Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and.
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Roda-Garcia
authors.affiliation: Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and.
authors.forename: Marcos
authors.initials: M
authors.lastname: Colebrook
authors.affiliation: Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain, CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Flores
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016247:Information Storage and Retrieval; D058977:Molecular Sequence Annotation / Q000379:methods; D017422:Sequence Analysis, DNA; D012984:Software