Data/hora: 16/06/2024 00:14:29

Provedor de dados: | 48
País: | Chile
Título: | Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
Autores: | Berthet,Nicolas; Descorps-Declère,Stéphane; Nkili-Meyong,Andriniaina Andy; Nakouné,Emmanuel; Gessain,Antoine; Manuguerra,Jean-Claude; Kazanji,Mirdad.
Data: | 2016-01-01
Ano: | 2016
Palavras-chave: | RNA viral genome; Next generation sequencing; SPAdes; Assembling genome; Amplification with phi29 polymerase.
Resumo: | 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 viral genomes. Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig. CONCLUSIONS: The proposed pipeline is able to overcome drawbacks due to the generation of chimeric reads during the amplification of viral RNA which considerably improves the assembling of full-length viral genomes.
Tipo: | Journal article
Idioma: | Inglês
Identificador: | http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100039
Editor: | Sociedad de Biología de Chile
Formato: | text/html
Fonte: | Biological Research  v.49 2016