IVA: accurate de novo assembly of RNA virus genomes

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

Fig. 1.

Example HIV-1 assemblies. Plots show the proportion of single base differences per mapped read compared to the IVA contig, the read depth and contigs from PRICE, Trinity and VICUNA aligned to the single IVA contig. The minimum read depth is 63

Fig. 2.

Comparison of assembly success. (a) For each segment of the reference, the longest matching contig was found. This plot shows the total length of these contigs for each assembly, as a percentage of the reference length. (b) Total assembly lengths, excluding contamination by only counting contigs that match the reference, as a percentage of the reference length