IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data | Zendy

Adrian BaezOrtega | Zendy; Fabián Lorenzo-Díaz | Zendy; Mariano Hernández | Zendy; Carlos Ignacio Gonzalez-Vila | Zendy; José Luis Roda García | Zendy; Marcos Colebrook | Zendy; Carlos Flores | Zendy

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IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data

Author(s) -

Adrian BaezOrtega,

Fabián Lorenzo-Díaz,

Mariano Hernández,

Carlos Ignacio Gonzalez-Vila,

José Luis Roda García,

Marcos Colebrook,

Carlos Flores

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv283

Subject(s) - ion semiconductor sequencing , sequence (biology) , computational biology , genome , whole genome sequencing , sequence analysis , computer science , biology , genetics , dna sequencing , gene

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.

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