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Updated: May 14, 2026
14:06
Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
Viral population analysis and minority-variant detection using short read next-generation sequencing.
Simon J Watson1, Matthijs R A Welkers, Daniel P Depledge
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Summary
This study introduces the QUASR pipeline to reduce sequencing errors in viral RNA analysis. QUASR improves accuracy for detecting low-frequency viral variants and understanding virus evolution.
Area of Science:
- Virology
- Genomics
- Bioinformatics
Background:
- RNA viruses exist as diverse populations of variants within hosts.
- Viral variant frequencies fluctuate due to evolutionary changes.
- Deep sequencing offers high-resolution analysis of viral populations.
Purpose of the Study:
- To develop and assess a bioinformatics pipeline (QUASR) for analyzing virus genome short reads.
- To minimize sequencing errors in deep-sequencing data for accurate variant detection.
- To enable post-mapping analysis of low-frequency viral variants.
Main Methods:
- Development of the Quality Assessment of Short Read (QUASR) Pipeline.
- Application of QUASR to analyze influenza virus (A/H1N1/09) genome dynamics.
- Utilizing data from Roche 454 GSFLX and Illumina GAIIx sequencing platforms.
Main Results:
- QUASR significantly reduces error-related noise in deep-sequencing datasets.
- The pipeline increases mapping accuracy and decreases erroneous mutations.
- Concordance between sequencing platforms enabled unambiguous minority-variant detection.
Conclusions:
- QUASR pipeline effectively minimizes sequencing errors in viral deep-sequencing data.
- The tool enhances the accuracy of identifying low-frequency viral variants.
- QUASR facilitates precise determination of virus population turnover and genome dynamics.
Related Concept Videos
03:00Next-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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...