IVA: accurate de novo assembly of RNA virus genomes

Bioinformatics
Martin HuntThomas D Otto

Abstract

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

References

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Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
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Citations

Oct 21, 2015·Frontiers in Microbiology·Saskia L SmitsAnita C Schürch
Jul 28, 2016·Journal of Virological Methods·Shambhu G AralaguppeUjjwal Neogi
Oct 4, 2016·Virus Research·Susana Posada-CespedesNiko Beerenwinkel
Aug 16, 2016·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·M SalmonaS Maylin
Sep 23, 2016·PLoS Neglected Tropical Diseases·Anismrita LahonRebecca Rico-Hesse
Apr 12, 2017·Genome Research·Jasmijn A BaaijensAlexander Schönhuth
Jun 8, 2017·The Journal of General Virology·Todd P KnutsonDouglas G Marthaler
Dec 29, 2017·PloS One·Alexis KafandoCécile L Tremblay
Jul 12, 2018·European Journal of Gastroenterology & Hepatology·Christina SølundNina Weis
Oct 7, 2017·The Journal of Experimental Medicine·Ellen M LeitmanPhilip J R Goulder
Jan 10, 2018·Scientific Reports·Mauricio Barrientos-SomarribasErik L L Sonnhammer
Feb 15, 2018·Archives of Virology·Steven Van BormBénédicte Lambrecht
Mar 1, 2019·Briefings in Bioinformatics·Martin AylingRichard M Leggett
Mar 22, 2019·Journal of Virology·Michelle WilleAeron C Hurt
Jul 18, 2017·Transboundary and Emerging Diseases·D SunD G Marthaler
Jun 23, 2020·Briefings in Bioinformatics·Sergey KnyazevAlexander Zelikovsky
Jul 24, 2020·The Journal of Infectious Diseases·Gu-Lung LinUNKNOWN RESCEU Investigators
Jan 14, 2017·Genome Announcements·Denise A MarstonJuan E Echevarría
Jul 29, 2017·Genome Announcements·Laura E BrettellStephen J Martin
Oct 3, 2017·Briefings in Bioinformatics·Gennady G FedoninAlexey D Neverov
Apr 1, 2020·Genomics & Informatics·Hyeon-Chun ParkSeung-Hyun Jung
Mar 3, 2017·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Heli HarvalaUNKNOWN ICONIC Consortium
Jun 13, 2017·PLoS Biology·François BlanquartUNKNOWN BEEHIVE collaboration
Jun 8, 2018·Virus Evolution·Chris WymantUNKNOWN BEEHIVE Collaboration
May 31, 2019·Bioinformatics·Jasmijn A BaaijensAlexander Schönhuth
Aug 3, 2016·Virus Evolution·Rebecca RoseMattia Prosperi

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

VICUNA
nucmer
PRICE
Trimmomatic
kmc
IVA
GAGE
IVA Virus Assembler
kmer
RATT

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