Related Experiment Video
Updated: Jul 16, 2025
09:26
Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
1.2K
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2
Hendrick Gao-Min Lim1,2, Yang C Fann3, Yuan-Chii Gladys Lee1
1Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031.
Briefings in Bioinformatics
|September 22, 2023
Summary
A new cloud workflow, COWID, efficiently analyzes SARS-CoV-2 genomic data. This tool offers scalable, reliable viral and variant identification at low cost, even with limited resources.
Area of Science:
- Genomics
- Bioinformatics
- Cloud Computing
Background:
- Analyzing extensive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic data presents challenges, especially with limited computational resources.
- Existing cloud platforms often require specialized configurations for novel pathogen research.
Purpose of the Study:
- To develop a cost-effective and efficient cloud-based workflow for SARS-CoV-2 genomic analysis.
- To repurpose existing cancer genomics cloud infrastructure for viral research.
Main Methods:
- Repurposed a cancer genomics cloud platform to create the Cloud Workflow for Viral and Variant Identification (COWID).
- Utilized the Common Workflow Language for scalable parallelization of genomic data analysis.
- Focused on reliable SARS-CoV-2 identification and variant detection.
Main Results:
- COWID processed raw sequencing data samples in under 5 minutes at a cost of US$0.01 per sample.
- Achieved scalable identification and reliable variant findings with no false-positive results.
- Outperformed contemporary methods in speed and accuracy.
Conclusions:
- COWID provides a user-friendly, time-efficient solution for SARS-CoV-2 genomic analysis during pandemics.
- The workflow is publicly available and accessible, requiring no prior programming knowledge.
- Repurposing cloud infrastructure offers a viable strategy for rapid response to emerging infectious diseases.
Related Concept Videos
02:02Genomics
36.4K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.4K
03:00Next-generation Sequencing
89.8K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
89.8K
01:57Sanger Sequencing
754.7K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
754.7K
01:11Genome-wide Association Studies-GWAS
13.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.6K
01:20Applications of Molecular Taxonomy
37
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
37
02:54Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K