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IVA: accurate de novo assembly of RNA virus genomes

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Title: IVA: accurate de novo assembly of RNA virus genomes
Authors: Hunt, M
Gall, A
Ong, SH
Brener, J
Ferns, B
Goulder, P
Nastouli, E
Keane, JA
Kellam, P
Otto, TD
Item Type: Journal Article
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
Issue Date: 15-Jul-2015
Date of Acceptance: 19-Feb-2015
URI: http://hdl.handle.net/10044/1/69575
DOI: https://dx.doi.org/10.1093/bioinformatics/btv120
ISSN: 1367-4803
Publisher: Oxford University Press (OUP)
Start Page: 2374
End Page: 2376
Journal / Book Title: Bioinformatics
Volume: 31
Issue: 14
Copyright Statement: © 2015 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Science & Technology
Life Sciences & Biomedicine
Technology
Physical Sciences
Biochemical Research Methods
Biotechnology & Applied Microbiology
Computer Science, Interdisciplinary Applications
Mathematical & Computational Biology
Statistics & Probability
Biochemistry & Molecular Biology
Computer Science
Mathematics
SEQUENCE DATA
SOFTWARE
Genome, Viral
HIV Infections
HIV-1
High-Throughput Nucleotide Sequencing
Humans
Influenza A virus
Influenza B virus
Influenza, Human
Polymerase Chain Reaction
RNA Viruses
Sequence Analysis, DNA
Software
01 Mathematical Sciences
06 Biological Sciences
08 Information and Computing Sciences
Bioinformatics
Publication Status: Published
Online Publication Date: 2015-02-28
Appears in Collections:Department of Medicine



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