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Next-generation Sequencing

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 Assembly

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 Sequencing

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...

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Related Experiment Video

Updated: Apr 22, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Enabling large-scale next-generation sequence assembly with Blacklight.

M Brian Couger¹, Lenore Pipes², Fabio Squina³

¹Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way. Stillwater, OK, 74078 USA.

Concurrency and Computation : Practice & Experience

|October 9, 2014

Summary

This summary is machine-generated.

Large-scale biological sequence analyses, including genomic and transcriptome assembly, were performed on the Blacklight XSEDE resource. These analyses advanced multiple scientific fields by leveraging high-performance computing for complex genomic data challenges.

Keywords:

NGS RNA-seq bioinformatics data-intensive computing de novo assembly genome genomics high-performance computing large shared memory computing metagenome primates transcriptome

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Related Experiment Videos

Last Updated: Apr 22, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Area of Science:

Computational Biology
Bioinformatics
Genomics

Background:

Biological sequence analysis presents significant computational challenges.
Access to large shared memory resources is crucial for complex bioinformatics tasks.

Purpose of the Study:

To conduct challenging biological sequence analyses using the Blacklight XSEDE resource.
To demonstrate the capabilities of Blacklight for diverse genomic and transcriptomic applications.

Main Methods:

Utilized the Blacklight XSEDE large shared memory resource.
Employed current bioinformatics tools for genomic sequence assembly, metagenomic assembly, transcriptome assembly, and sequencing error correction.
Developed a new parallel command execution program for specific analyses.

Main Results:

Successfully performed a variety of challenging biological sequence analyses on diverse datasets.
Included analyses of fungal, microbial, microbiome, and primate sequence data (short-read and long-read).
Demonstrated significant advances in genomic and transcriptomic data analysis.

Conclusions:

The Blacklight XSEDE resource offers ease of use, versatility, and unique capabilities for scientific analysis.
High-performance computing resources, supported by XSEDE, are powerful tools for addressing complex scientific problems in genomics and transcriptomics.