SciELO - Scientific Electronic Library Online

 
vol.49Potential role of marine algae extract on 3T3-L1 cell proliferation and differentiation: an in vitro approachUpregulation of MiR-196a promotes cell proliferation by downregulating p27kip1 in laryngeal cancer índice de autoresíndice de assuntospesquisa de artigos
Home Pagelista alfabética de periódicos  

Serviços Personalizados

Journal

Artigo

Indicadores

Links relacionados

  • Em processo de indexaçãoCitado por Google
  • Não possue artigos similaresSimilares em SciELO
  • Em processo de indexaçãoSimilares em Google

Compartilhar


Biological Research

versão impressa ISSN 0716-9760

Resumo

BERTHET, Nicolas et al. Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data. Biol. Res. [online]. 2016, vol.49, pp.1-8. ISSN 0716-9760.  http://dx.doi.org/10.1186/s40659-016-0099-y.

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.

Palavras-chave : RNA viral genome; Next generation sequencing; SPAdes; Assembling genome; Amplification with phi29 polymerase.

        · texto em Inglês     · Inglês ( pdf )

 

Creative Commons License Todo o conteúdo deste periódico, exceto onde está identificado, está licenciado sob uma Licença Creative Commons