ArticleBiological research2016
Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data.
Article in Biological research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Genome Sequencing of Historical Encephalomyocarditis Viruses from South Africa Links the Historical 1993/4 Savanna Elephant (Pathogens (Basel, Switzerland) · 2024Article
- ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.PLoS computational biology · 2021Article
- A Second Genome Sequence of an Enterovirus C99 Detected in a Healthy Chimpanzee.Microbiology resource announcements · 2020Article
- Complete Genome Sequences of Igbo-Ora and Babanki Alphavirus Strains Isolated in the Central African Republic in the 1960s and 1970s.Microbiology resource announcements · 2019Article
- Complete Genome Sequence of an Equine Arteritis Virus Strain Isolated from a Lipizzaner Stallion in 2015 in Serbia.Microbiology resource announcements · 2019Article
- Complete Genome Sequence of the Tataguine Virus, Isolated in the Central African Republic in 1972 from a Human with an Acute Febrile Syndrome.Microbiology resource announcements · 2019Article
- Complete Genome Sequences of Two Chikungunya Viruses Isolated in the Central African Republic in the 1970s and 1980s.Genome announcements · 2017Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNew 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.
findingsThree 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.
conclusionsThe 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.
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