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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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.
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.
Sanger Sequencing01:57

Sanger Sequencing

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...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Genomics02:02

Genomics

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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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Consed: a graphical editor for next-generation sequencing.

David Gordon1, Phil Green

  • 1Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

Bioinformatics (Oxford, England)
|September 3, 2013
PubMed
Summary
This summary is machine-generated.

The consed software has been updated with bamScape to efficiently handle large DNA sequencing datasets, improving error correction and data analysis for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • DNA sequencing throughput has increased dramatically.
  • Existing graphical interfaces struggle with large datasets.
  • Efficient error correction and data visualization are critical.

Purpose of the Study:

  • To adapt the consed software for handling large DNA sequencing datasets.
  • To develop a viewer for efficient identification and editing of problematic read regions.
  • To enhance graphical editing capabilities for large-scale genomic data analysis.

Main Methods:

  • Developed bamScape, a viewer for billion-read BAM files.
  • Integrated bamScape with the consed graphical editor.
  • Implemented features for direct reference sequence editing, variant/error detection, and annotation track display.

Main Results:

  • bamScape efficiently identifies and displays problem areas in large BAM files.
  • The adapted consed allows full-feature editing of large datasets with low memory requirements.
  • New features include simultaneous processing of read groups and batch processing capabilities.

Conclusions:

  • The updated consed, featuring bamScape, addresses the challenges of analyzing large DNA sequencing datasets.
  • The enhancements enable efficient error correction, variant detection, and reference sequence editing.
  • These improvements are crucial for advancing genomic research with high-throughput sequencing data.