Applications of Metagenomics and Viral Genomics to Investigating Diseases of Livestock

2021 ◽  
pp. 37-48
Author(s):  
Barbara Brito Rodriguez ◽  
Barbara Brito Rodriguez
Keyword(s):  
Viral Genomics

Running the Titan_Illumina_PE Workflow on Terra.bio v1

2021 ◽  
Author(s):  
Jill V Hagey ◽  
Kevin Libuit ◽  
Frank J Ambrosio ◽  
Technical Outreach and Assistance for States Team
Keyword(s):  
Public Health ◽  
Technical Assistance ◽  
File Format ◽  
Technical Documentation ◽  
Video Instruction ◽  
The Public ◽  
Viral Genomics ◽  
Genomic Characterization ◽  
Primer Sequence

The Titan_Illumina_PE workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_Illumina_PE was written specifically to process Illumina paired-end (PE) read data. Input reads are assumed to be the product of sequencing tiled PCR-amplicons designed for the SARS-CoV-2 genome. The most common read data analyzed by the Titan_Illumina_PE workflow are generated with the ARTIC V3 protocol. However, alternative primer schemes such as the QIAseq Primer Panel are also suitable for this workflow. The primer sequence coordinates of the PCR scheme utilized must be provided in BED format along with the raw Illumina read data. Upon initiating a Titan_Illumina_PE job, the input primer scheme coordinates and raw paired-end Illumina read data provided for each sample will be processed to perform consensus genome assembly, infer the quality of both raw read data and the generated consensus genome, and assign lineage or clade designations as outlined in the Titan_Illumina_PE data workflow diagram below. Additional technical documentation for the Titan_Illumina_PE workflow is available at: https://public-health-viral-genomics-theiagen.readthedocs.io/en/latest/titan_workflows.html#titan-workflows-for-genomic-characterization Required input data for Titan Illumina PE: Illumina paired-end read data (forward and reverse FASTQ files per sample) Primer sequence coordinates of the PCR scheme utilized in BED file format Video Instruction: Theiagen Genomics: Titan Genomic Characterization https://www.youtube.com/watch?v=zP9I1r6TNrw Theiagen Genomics: Titan Outputs QC https://www.youtube.com/watch?v=Amb-8M71umw For technical assistance please contact us at: [email protected]

Viral Genomics and Evolution: The Fascinating Story of Dairy Phages

2021 ◽  
pp. 171-187
Author(s):  
Marine Feyereisen ◽  
Katherine Lavelle ◽  
Tadhg O'Sullivan ◽  
Douwe van Sinderen ◽  
Jennifer Mahony
Keyword(s):  
Viral Genomics

scholarly journals viruSITE—integrated database for viral genomics

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw162 ◽  
Author(s):  
Matej Stano ◽  
Gabor Beke ◽  
Lubos Klucar
Keyword(s):  
Viral Genomics

Running the Titan_ONT Workflow on Terra.bio v1

2021 ◽  
Author(s):  
Francis J J. Ambrosio ◽  
Jill V Hagey ◽  
Kevin Libuit ◽  
Technical Outreach and Assistance for States Team
Keyword(s):  
Public Health ◽  
Technical Assistance ◽  
Technical Documentation ◽  
The Public ◽  
Viral Genomics ◽  
Oxford Nanopore ◽  
Genomic Characterization ◽  
Data Files ◽  
Primer Sequence

The Titan_ONT workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_ONT was written specifically to process basecalled and demultiplexed Oxford Nanopore Technology (ONT) read data. Input reads are assumed to be the product of sequencing ARTIC V3 tiled PCR-amplicons designed for the SARS-CoV-2 genome. Upon initiating a Titan_ONT run, input read data provided for each sample will be processed to perform consensus genome assembly, infer the quality of both raw read data and the generated consensus genome, and assign lineage or clade designations as outlined in the Titan_ONT data workflow diagram below. Additional technical documentation for the Titan_ONT workflow is available at: https://public-health-viral-genomics-theiagen.readthedocs.io/en/latest/titan_workflows.html#titan-workflows-for-genomic-characterization Required input data for Titan_ONT: Basecalled and demultiplexed ONT read data files (single FASTQ file per sample) Primer sequence coordinates of the PCR scheme utilized in BED file format Titan_ONT has not been written to process FAST5 files Video Instruction: Theiagen Genomics: Titan Genomic Characterization https://www.youtube.com/watch?v=zP9I1r6TNrw Theiagen Genomics: Titan Outputs QC https://www.youtube.com/watch?v=Amb-8M71umw For technical assistance please contact us at: [email protected]

scholarly journals SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 526 ◽  
Author(s):  
Mohammed Uddin ◽  
Farah Mustafa ◽  
Tahir A. Rizvi ◽  
Tom Loney ◽  
Hanan Al Suwaidi ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Vaccine Development ◽  
Intervention Development ◽  
Severe Pneumonia ◽  
Therapeutic Interventions ◽  
Current Status ◽  
The Novel ◽  
Comprehensive Overview ◽  
Viral Genomics ◽  
Map Analysis

The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 virus that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress, and fatality. To address this global crisis, up-to-date information on viral genomics and transcriptomics is crucial for understanding the origins and global dispersion of the virus, providing insights into viral pathogenicity, transmission, and epidemiology, and enabling strategies for therapeutic interventions, drug discovery, and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.

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