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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....

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Updated: Sep 28, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi-sample

Hui Wang¹, Shenghan Gao², Yu Liu¹

¹MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China.

Ecology and Evolution

|March 28, 2022

Summary

This summary is machine-generated.

Developing polymorphic simple sequence repeat (SSR) markers is challenging. This study presents a pipeline using multi-sample genomic data for rapid SSR marker development, improving efficiency for ecological and evolutionary studies.

Keywords:

microsatellite molecular marker next‐generation sequencing resequencing short tandem repeats threatened species

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Pyrosequencing: A Simple Method for Accurate Genotyping

Pyrosequencing: A Simple Method for Accurate Genotyping

Published on: January 8, 2008

Area of Science:

Genomics
Molecular Ecology
Conservation Genetics

Background:

Simple sequence repeats (SSRs) are valuable genetic markers in ecology, evolution, and conservation.
Developing polymorphic SSR markers is a significant limitation, often requiring extensive experimental validation.
Next-generation sequencing (NGS) offers potential for rapid SSR development, but single-individual data necessitates redundant validation.

Purpose of the Study:

To design and validate a pipeline for the rapid development of polymorphic SSR markers using multi-sample genomic data.
To enhance the efficiency and reduce experimental effort in SSR marker development.
To provide a cost-effective alternative to traditional methods, especially for species with limited genomic resources.

Main Methods:

A bioinformatic pipeline was developed to genotype multiple individuals from resequencing data.
Highly polymorphic SSRs were identified computationally prior to experimental validation.
The pipeline was applied to the brown eared-pheasant (Crossoptilon mantchuricum), a species with low genomic diversity.

Main Results:

The pipeline successfully developed 20 highly polymorphic SSR markers for the brown eared-pheasant.
The developed SSR markers exhibited significantly higher average allele numbers compared to the genomic average.
Optimal results for SSR mining were achieved with approximately 10 individuals and ~10X sequencing depth, even for low-diversity species.

Conclusions:

The developed pipeline significantly improves the efficiency of polymorphic SSR marker development from multi-sample NGS data.
The pipeline is effective even for species with low genetic diversity, such as the brown eared-pheasant.
NGS data from optimized individual numbers and sequencing depth can serve as a reference genome, offering a valuable tool for ecological and evolutionary research.