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 immunodefic

SUBMITTER: Hunt M 

PROVIDER: S-EPMC4495290 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature