Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data.

ABSTRACT:

Background

New sequencing technologies have opened the way to the discovery and the characterization of pathogenic viruses in clinical samples. However, the use of these new methods can require an amplification of viral RNA prior to the sequencing. Among all the available methods, the procedure based on the use of Phi29 polymerase produces a huge amount of amplified DNA. However, its major disadvantage is to generate a large number of chimeric sequences which can affect the assembly step. The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes.

Findings

Three different assembly softwares (ABySS, Ray and SPAdes) were tested for their ability to correctly assemble the full-length of

SUBMITTER: Berthet N 

PROVIDER: S-EPMC5015205 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature