Adrian Baez-Ortega1, Fabian Lorenzo-Diaz2, Mariano Hernandez3, Carlos Ignacio Gonzalez-Vila1, Jose Luis Roda-Garcia4, Marcos Colebrook4, Carlos Flores5. 1. Information Technology Department, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain. 2. 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. 3. Applied Genomics Group (G2A), Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (CIBICAN), Universidad de La Laguna, Santa Cruz de Tenerife, Spain. 4. Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and. 5. 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.
Abstract
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: mcolesan@ull.edu.es or cflores@ull.edu.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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: mcolesan@ull.edu.es or cflores@ull.edu.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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