The IonGAP Project

What's IonGAP?

IonGAP is a publicly available integrated pipeline designed for the assembly and subsequent analysis of Ion Torrent bacterial sequence data. Both its components and their configuration are based on a research process aimed to discover the optimal combination of tools for obtaining good results from single-end reads generated by the Ion Torrent PGM sequencer.

IonGAP arises from a research project at the Universidad de La Laguna (University of La Laguna), being initially conceived as a tool for the genomics experts of the Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (University Institute of Tropical Diseases and Public Health of the Canary Islands). You can access the full research documentation here.

Currently, IonGAP is a joint project between the Instituto Tecnológico y de Energías Renovables (ITER, Institute of Technology and Renewable Energies), the Universidad de La Laguna, and the Servicio Canario de la Salud (Canary Health Service). All these entities are based in Tenerife, Canary Islands, Spain. The whole platform runs on ITER's Teide-HPC, which is the second most powerful computer in Spain at present.

In order to discover the functionalities of the platform, please consult the Tools and Features section. If you are interested in benefiting from a dedicated computing infrastructure with extended resources, please contact us.

The IonGAP Group

IonGAP is a multidisciplinary project developed thanks to people from different institutions:

Instituto Tecnológico y de Energías Renovables (ITER)
Hospital Universitario Nuestra Señora de Candelaria (HUNSC)
Universidad de La Laguna (ULL)
Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES)

Our current group members are:

Adrian Baez-Ortega, MSc in Computer Science (ITER)
Marcos Colebrook, PhD in Operations Research (ULL)
Carlos Flores, PhD in Biology (HUNSC, ULL, CIBERES)
Carlos Gonzalez-Vila, MSc in Computer Science (ITER)
Mariano Hernandez, PhD in Biology (ULL)
Fabian Lorenzo-Diaz, PhD in Biology (HUNSC, ULL)
Jose Luis Roda-Garcia, PhD in Computer Science (ULL)

Special thanks are due to the members of the ETSII Computing Centre (Universidad de La Laguna) and of the High Performance Computing Section of the Information Technology Department of the ITER, for their help in the deployment of the initial and present versions of the platform, respectively.

Evolution and Use

IonGAP is being used by an increasing number of professionals from different countries and institutions. The total number of completed projects is displayed below, together with the location of our latest users.

1529 projects completed

The history of upgrades and fixes applied to the platform is detailed below.

IonGAP Changelog

2017/01/10

Computational resources extended.

2015/11/07

Added support for .fq (FASTQ), .fna and .fas (FASTA) file extensions.
User manual updated to include list of supported extensions.

2015/08/06

Platform RAM extended to 50 GB and computing power doubled to allow the assembly of challenging bacterial genomes.

2015/03/09

Two new programs integrated into the Comparative Genomics module: Cortex for variant calling, and TRAMS for SNP annotation (from raw reads).
'Tools and Features' updated: Cortex and TRAMS added to the Comparative Genomics module table (with examples).
Project form and manual updated to include variant calling and SNP annotation.
HTML project summary file updated to include variant calling and SNP annotation.
Padded contigs FASTA file added to the Assembly module results.

2015/02/18

Support for SRA files implemented.
FTP URL option added to the project form.
Project form updated to clarify the restrictions on input data.
User manual updated.

2015/01/29

Fixed problem when aligning to a very fragmented reference genome.

2015/01/14

'The IonGAP Project' updated: geographic map of recent users and changelog added.

2015/01/12

'Tools and Features' updated: new table for the Genome Assembly module and galleries of graphical examples added.

2015/01/09

New summary file included into project results ('Projectname_Summary.html').

2015/01/08

Dropbox URL option added to the project form.
Problem with unpackaging of .tar.bz2 files fixed.
User manual updated.

2014/12/02

Test dataset added.
User manual and home page updated.

2014/11/28

IonGAP platform released to the public.

Citing IonGAP

If you use results from IonGAP, please cite us:

Adrian Baez-Ortega, Fabian Lorenzo-Diaz, Mariano Hernandez, Carlos Ignacio Gonzalez-Vila, Jose Luis Roda-Garcia, Marcos Colebrook, and Carlos Flores
IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data
Bioinformatics, 31(17), 2015, 2870–2873
doi: 10.1093/bioinformatics/btv283