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OMIC
08642

IonGAP

A publicly available web platform designed for the analysis of whole bacterial genomes by using Ion Torrent sequence data. Besides assembly, IonGAP 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.

Specifications

Interface:
Web user interface
Restrictions to use:
None
Biological technology:
Life Technologies
Computer skills:
Basic
Stability:
Stable
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Documentation & support

Maintainer

  • IonGAP <iongap.adm at gmail.com>

Credits

Institution(s)

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, Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain

Publications

  • (Baez-Ortega et al., 2015) IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data. Bioinformatics.
    PMID: 25953799

Classification

Literature

  • (Magoc et al., 2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics.
    PMID: 23665771
  • (Miller et al., 2010) Assembly algorithms for next-generation sequencing data. Genomics.
    PMID: 20211242
  • (Narzisi and Mishra, 2011) Comparing de novo genome assembly: the long and short of it. PloS one.
    PMID: 21559467
  • (Henson et al., 2012) Next-generation sequencing and large genome assemblies. Pharmacogenomics.
    PMID: 22676195
  • (Kleftogiannis et al., 2013) Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures. PloS one.
    PMID: 24086547
  • (Nagarajan and Pop, 2013) Sequence assembly demystified. Nature reviews Genetics.
    PMID: 23358380
  • (Bradnam et al., 2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience.
    PMID: 23870653
  • (Salzberg et al., 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.
    PMID: 22147368
  • (Utturkar et al., 2014) Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. Bioinformatics.
    PMID: 24930142
  • (Alkan et al., 2011) Limitations of next-generation genome sequence assembly. Nature methods.
    PMID: 21102452
  • (Love et al., 2016) Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC genomics.
    PMID: 26944054

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