IVA: accurate de novo assembly of RNA virus genomes.
BACKGROUND
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.


METHODS
The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
Martin
M
Hunt
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
Astrid
A
Gall
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
Swee Hoe
SH
Ong
Department of Paediatrics, University of Oxford, Oxford, UK.
Jacqui
J
Brener
Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK and.
Bridget
B
Ferns
Department of Paediatrics, University of Oxford, Oxford, UK.
Philip
P
Goulder
Department of Virology, University College London Hospital NHS Foundation Trust, London, UK.
Eleni
E
Nastouli
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
Jacqueline A
JA
Keane
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.
Paul
P
Kellam
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
Thomas D
TD
Otto
D016679:Genome, Viral; D015658:HIV Infections / Q000235:genetics / Q000821:virology; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D009980:Influenza A virus / Q000235:genetics* / Q000302:isolation & purification; D009981:Influenza B virus / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000235:genetics / Q000821:virology; D016133:Polymerase Chain Reaction / Q000379:methods; D012328:RNA Viruses / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software