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RNA-seq

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...

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Updated: Dec 25, 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

MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data.

Liang Guo^1,2, Quan Yang^1,2,3, Jing-Wen Yang^1,2

¹Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China.

Ecology and Evolution

|March 27, 2020

Summary

MultiplexSSR pipeline efficiently develops highly polymorphic simple sequence repeats (SSRs) from sequencing data for conservation genetics. This method enhances SSR marker development, offering a cost-effective alternative to traditional approaches.

Keywords:

multiplex SSR‐PCR pedigree construction pipeline resequencing

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Area of Science:

Genetics
Bioinformatics
Molecular Biology

Background:

Simple sequence repeats (SSRs) offer advantages in conservation genetics despite declining research.
Next-generation sequencing (NGS) primarily focuses on single nucleotide polymorphisms, overlooking SSR potential.
Developing SSR markers traditionally is time-consuming and costly.

Purpose of the Study:

To establish an end-to-end pipeline, MultiplexSSR, for developing multiplex PCR assays for SSRs from resequencing data.
To investigate SSR distribution, genotyping/allelotyping error profiles, and allele length range saturation.
To validate the pipeline's robustness and cost-effectiveness for marker development.

Main Methods:

Developed the MultiplexSSR pipeline for batch development of multiplex PCR assays.
Analyzed SSR distribution, error rates (genotyping/allelotyping), and allele length variation.
Utilized in silico PCR for primer specificity and allele number for polymorphism selection.

Main Results:

98% of SSRs were less than 100 bp; dimeric patterns showed higher error rates.
Allelotype error rates were lower than genotyping error rates.
Allele length range saturated around 10 individuals; pipeline demonstrated robustness and cost-effectiveness.

Conclusions:

The MultiplexSSR pipeline effectively bridges NGS data and multiplex SSR-PCR marker development.
Developed SSR markers exhibit high polymorphism, stability, and reduced genotyping costs.
The pipeline enables efficient SSR marker development using low-depth resequencing data.