pTrimmer

pTrimmer trims primer sequences from multiplex amplicon sequencing (MAS) and targeted deep sequencing reads to enable accurate downstream detection of genetic variation.

Key Features:

• High Sensitivity and Accuracy: Achieves 99.96% sensitivity and 97.38% accuracy for primer trimming, compared with cutPrimers (70.85% sensitivity, 58.73% accuracy).
• Efficient Algorithmic Approach: Integrates k-mers and the Needleman-Wunsch algorithm to identify and remove primers while accommodating sequencing errors.
• Scalability and Speed: Designed to handle thousands of primer pairs, reported ~370× faster than cutPrimers and ~17,000× faster per thread than cutadapt, trimming 2,158 primer pairs from 11 million reads (Illumina PE 150 bp) in 37 seconds using ≤100 MB memory.
• Clinical and Research Utility: Applicable to clinical sample processing and research workflows for reliable mutational information extraction from multiplex deep sequencing data.
• Comparative Advantages: Exhibits superior sensitivity and specificity relative to similar tools such as cutPrimers and cutadapt.

Scientific Applications:

• Multiplex amplicon sequencing (MAS) preprocessing: Removal of primer sequences to improve variant calling accuracy from MAS data.
• High-throughput targeted genome sequencing: Primer trimming for large-scale target-enrichment and amplicon-based sequencing projects.
• Clinical variant detection: Processing of patient-derived sequencing reads to support clinical genetic variation analysis.
• Large-scale primer management: Handling thousands of primer pairs in large sequencing datasets for downstream analysis.

Methodology:

Combines k-mer matching with the Needleman-Wunsch alignment algorithm to detect and trim primer sequences from sequencing reads while tolerating sequencing errors.