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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Genomics02:02

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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...
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Flow Cytometry01:23

Flow Cytometry

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The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
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Sanger Sequencing01:57

Sanger Sequencing

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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...
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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud.

Ryan P Seaman1, Ross Campbell2, Valena Doe3

  • 1MDI Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA.

Briefings in Bioinformatics
|June 28, 2024
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Summary
This summary is machine-generated.

This study introduces a cloud-based learning module for de novo transcriptome assembly. It teaches computational workflows and efficient cloud resource use, reducing the need for on-site computing in bioinformatics.

Keywords:
annotationassemblycloud computingnextflowtraining moduletranscriptome

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biomedical researchers require new skills to leverage cloud computing resources.
  • Cloud platforms offer powerful, cost-effective solutions for data access and analysis.
  • Traditional on-site computing can be a barrier for advanced bioinformatics tasks.

Purpose of the Study:

  • To develop an interactive, cloud-based training module for de novo transcriptome assembly.
  • To demonstrate the use of Nextflow for computational workflows.
  • To teach cost- and resource-efficient utilization of Google Cloud Platform services.

Main Methods:

  • Development of a learning module within the NIGMS Sandbox for Cloud-based Learning platform.
  • Utilizing de novo transcriptome assembly as a biological case study.
  • Integration with Google Cloud Platform for interactive data access and analysis.

Main Results:

  • The module effectively teaches Nextflow computational workflows.
  • Demonstrates efficient use of cloud resources for bioinformatics tasks.
  • Highlights the accessibility and reduced necessity of on-site computing.

Conclusions:

  • Cloud-based training modules are effective for upskilling biomedical researchers.
  • De novo transcriptome assembly can be successfully taught using cloud infrastructure.
  • The NIGMS Sandbox provides a valuable resource for cloud-based bioinformatics education.