IonGAP：用于Ion Torrent序列数据的综合细菌基因组分析

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.

作者信息

Baez-Ortega Adrian, Lorenzo-Diaz Fabian, Hernandez Mariano, Gonzalez-Vila Carlos Ignacio, Roda-Garcia Jose Luis, Colebrook Marcos, Flores Carlos

机构信息

Information Technology Department, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.

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.

出版信息

Bioinformatics. 2015 Sep 1;31(17):2870-3. doi: 10.1093/bioinformatics/btv283. Epub 2015 May 6.

DOI:10.1093/bioinformatics/btv283

PMID:25953799

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.

摘要

未标注

我们推出了IonGAP，这是一个公开可用的网络平台，旨在使用Ion Torrent序列数据对细菌全基因组进行分析。除了组装之外，它还基于广泛使用的FASTQ、BAM和SRA文件格式，集成了各种比较基因组学、注释和细菌分类程序。使用不同数据集进行的基准测试证明，IonGAP是一个快速、强大且易于使用的生物信息学工具。通过发布这个平台，我们旨在将低成本的细菌基因组分析转化应用于医疗保健、农业食品和制药行业的微生物预防与控制。