Format

Send to

Choose Destination
Bioinformatics. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.

IVA: accurate de novo assembly of RNA virus genomes.

Author information

1
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
2
Department of Paediatrics, University of Oxford, Oxford, UK.
3
Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK and.
4
Department of Virology, University College London Hospital NHS Foundation Trust, London, UK.
5
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK, Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK and.

Abstract

MOTIVATION:

An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and polymerase chain reaction amplification process of current methods.

RESULTS:

We developed a new de novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

AVAILABILITY AND IMPLEMENTATION:

The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

PMID:
25725497
PMCID:
PMC4495290
DOI:
10.1093/bioinformatics/btv120
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center