Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data
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Summary
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.
- Type
- article
- Published
- 2016-09-07
- Cited by
- 11
- References
- 22
- Access
- Open access
- OpenAlex
- https://openalex.org/W27605096
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:7298910
Keywords
Humanities, Art
References
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- Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
- Removing Noise From Pyrosequenced Amplicons
- QUAST: quality assessment tool for genome assemblies
- Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- MRBAYES: Bayesian inference of phylogenetic trees
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- At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
- Fast gapped-read alignment with Bowtie 2
- No evidence for viral sequences in five lepidic adenocarcinomas (former “BAC”) by a high-throughput sequencing approach
- ViromeScan: a new tool for metagenomic viral community profiling
Cited by
- Complete Genome Sequences of Two Chikungunya Viruses Isolated in the Central African Republic in the 1970s and 1980s
- Molecular characterization of complete genome of a canine distemper virus associated with fatal infection in dogs in Gabon, Central Africa.
- Detection and characterisation of novel vector-borne viruses in Mozambique
- Vector-borne viruses and their detection by viral metagenomics
- Complete Genome Sequence of the Tataguine Virus, Isolated in the Central African Republic in 1972 from a Human with an Acute Febrile Syndrome
- Complete Genome Sequence of an Equine Arteritis Virus Strain Isolated from a Lipizzaner Stallion in 2015 in Serbia
- Complete Genome Sequences of Igbo-Ora and Babanki Alphavirus Strains Isolated in the Central African Republic in the 1960s and 1970s
- A Second Genome Sequence of an Enterovirus C99 Detected in a Healthy Chimpanzee
- ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach
- Genome Sequencing of Historical Encephalomyocarditis Viruses from South Africa Links the Historical 1993/4 Savanna Elephant (Loxodonta africana) Outbreak to Cryptic Mastomys Rodents
- Critical ACTUAL TRENDS IN WATER ECOSYSTEM BIOLOGY DEVELOPMENT
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