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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.
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Genome Annotation and Assembly

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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.

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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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.
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Updated: Aug 23, 2025

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

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A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly.

Ou Wang¹, Xiaofang Cheng², Radoje Drmanac³

¹BGI-Shenzhen, Shenzhen, Guangdong Province, People's Republic of China.

Methods in Molecular Biology (Clifton, N.J.)

|November 6, 2022

Summary

We introduce single-tube long fragment read (stLFR), a cost-effective whole-genome sequencing method. This DNA co-barcoding strategy simplifies library preparation for detecting all genetic variations and assembling genomes.

Keywords:

Co-barcoding Combinatorial barcode beads Diploid de novo assembly Experimental haplotyping Long DNA molecules Phasing Whole-genome sequencing

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Whole-genome sequencing and physical haplotyping are crucial for understanding genetic variations.
Existing methods like LFR (long fragment read) can be complex and costly.
There is a need for accessible and efficient techniques for comprehensive genome analysis.

Purpose of the Study:

To describe a novel, simplified method for whole-genome sequencing and physical haplotyping called single-tube long fragment read (stLFR).
To demonstrate the utility of stLFR for detecting and phasing genetic variations, including structural variations.
To highlight stLFR's potential for genome assembly and scaffolding.

Main Methods:

stLFR employs a DNA co-barcoding strategy using magnetic beads for virtual compartmentalization.
A split-and-pool process generates numerous copies of unique barcodes on each bead.
Libraries are prepared in a single tube, compatible with standard second-generation sequencing platforms.

Main Results:

stLFR enables whole-genome sequencing and physical haplotyping with high efficiency and low cost (~$30 per sample).
The method allows for the detection and phasing of all genetic variations, including large structural variations.
stLFR data facilitates scaffolding of contigs and de novo genome assembly.

Conclusions:

stLFR offers a simple, accessible, and cost-effective approach for advanced genomic analyses.
This technique significantly enhances the ability to detect and phase genetic variations across the genome.
stLFR is a valuable tool for comprehensive genome sequencing, haplotyping, and assembly in standard labs.