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A de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. IVA produces significantly higher quality assemblies than existing approaches.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Biological technology:
Illumina
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Martin Hunt <iva at sanger.ac.uk>

Institution(s)

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK

Funding source(s)

This work was supported by researchers at the NIHR University College London Hospitals Biomedical Research Centre, the HICF and ICONIC grants [HICF-T5-344/WT098608], the Wellcome Trust [grant 098051], the European Union 7th framework EVIMalaR [to T.O.] and Global Health [grant number OPP1084362 to S.H.O.].

  • (Hunt et al., 2015) IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics.
    PMID: 25725497
  • (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

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