Comparison of sequence reads obtained from three next-generation sequencing platforms
Shingo Suzuki1, Naoaki Ono, Chikara Furusawa
1Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Suita, Osaka, Japan.
Plos One
|May 26, 2011
Summary
Next-generation sequencing platforms vary in data quality and SNP detection performance. Roche Genome Sequencer FLX (FLX) showed better SNP detection with less sequence coverage compared to Illumina Genome Analyzer (GA) and Applied Biosystems SOLiD (SOLiD) systems.
Area of Science:
- Genomics
- Bioinformatics
- Next-Generation Sequencing
Background:
- Next-generation sequencing (NGS) technologies offer rapid and cost-effective DNA sequencing.
- Evaluating the quality of sequence reads is crucial for assessing NGS performance.
Purpose of the Study:
- To analyze sequence read quality and single nucleotide polymorphism (SNP) detection performance across three commercial NGS platforms.
- To compare the accuracy, sequence bias, and SNP detection capabilities of Roche Genome Sequencer FLX (FLX), Illumina Genome Analyzer (GA), and Applied Biosystems SOLiD (SOLiD) systems.
Main Methods:
- Genomic DNA from Escherichia coli strain DH1 was sequenced using FLX, GA, and SOLiD platforms.
- Sequence reads were aligned to the reference genome (E. coli DH1) to assess accuracy and bias.
- Sequence differences between E. coli strains (DH1 and W3110) were identified to evaluate SNP detection.
Main Results:
- SOLiD generated the largest fraction of unaligned reads ('junk' data).
- GA data exhibited the poorest sequence accuracy, indicating lower fidelity.
- SNP detection was comparable across platforms, but FLX required significantly less sequence coverage.
Conclusions:
- NGS platforms differ in read quality, with SOLiD and GA showing specific limitations in alignment and accuracy, respectively.
- FLX demonstrated efficient SNP detection with lower sequence coverage requirements.
- These findings provide critical insights into NGS platform performance for genomic analysis and SNP discovery.
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