IVA

The software tool IVA is a de novo assembler specifically designed for sequencing data from RNA viruses, which pose challenges due to viral population diversity and uneven read depth caused by amplification bias. IVA was tested on datasets from 140 human immunodeficiency virus-1 or influenza-virus-infected samples and outperformed other virus de novo assemblers.

Topic

Sequence analysis;Sequence assembly;Sequence composition, complexity and repeats

Detail

Operation: Sequence assembly;Repeat sequence analysis
Software interface: Command-line user interface
Language: R;Perl;Python
License: GNU General Public License, version 3
Cost: Free
Version name: v1.0.11
Credit: NIHR University College London Hospitals Biomedical Research Centre, the HICF and ICONIC grants, the Wellcome Trust, the European Union 7th framework EVIMalaRand Global Health.
Input: -
Output: -
Contact: iva@sanger.ac.uk
Collection: -
Maturity: -

Publications

IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, et al. IVA: accurate de novo assembly of RNA virus genomes. IVA: accurate de novo assembly of RNA virus genomes. 2015; 31:2374-6. doi: 10.1093/bioinformatics/btv120
https://doi.org/10.1093/bioinformatics/btv120
PMID: 25725497
PMC: PMC4495290

Download and documentation

Source: https://github.com/sanger-pathogens/iva/archive/v1.0.3.tar.gz
Documentation: https://github.com/sanger-pathogens/iva/wiki
Home page: http://sanger-pathogens.github.io/iva/
Data: https://github.com/sanger-pathogens/iva/wiki/Assembly-test-data
Links: https://github.com/sanger-pathogens/iva/wiki/Installation-notes-for-Ubuntu

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