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SeqPurge: highly-sensitive adapter trimming for paired-end NGS data.
Marc Sturm1, Christopher Schroeder2, Peter Bauer2
1Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany. marc.sturm@med.uni-tuebingen.de.
BMC Bioinformatics
|May 11, 2016
Summary
SeqPurge is a new adapter trimming tool for next-generation sequencing (NGS) data. It effectively removes adapter sequences, improving data quality and reducing spurious variant calls in paired-end sequencing.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Adapter trimming is crucial for next-generation sequencing (NGS) data preprocessing.
- Existing tools struggle to remove all adapter sequences, potentially causing errors in amplicon-based data analysis.
- Adapter contamination can lead to spurious variant calls, compromising data integrity.
Purpose of the Study:
- To develop a highly sensitive adapter trimmer for paired-end Illumina sequencing data.
- To address the limitations of current tools in removing residual adapter sequences.
- To improve the accuracy of variant calling by minimizing adapter contamination.
Main Methods:
- Developed SeqPurge, a novel adapter trimmer utilizing a probabilistic approach.
- Leveraged the overlap between forward and reverse reads for adapter sequence detection.
- Evaluated SeqPurge's sensitivity, specificity, and error tolerance against existing tools.
Main Results:
- SeqPurge demonstrates high sensitivity in detecting even single-base adapter sequences.
- Achieved up to a 90% reduction in remaining adapter bases compared to other tools.
- Exhibited superior error tolerance in simulations, outperforming other adapter trimmers.
Conclusions:
- SeqPurge offers high sensitivity and error tolerance for adapter trimming.
- Its performance is comparable to state-of-the-art tools in specificity and runtime.
- SeqPurge is an excellent choice for preprocessing paired-end NGS data, offering additional quality control features.
