CASPER

CASPER merges overlapping forward and reverse paired-end sequencing reads to produce virtually elongated, higher-fidelity sequences for high-throughput amplicon sequencing, improving downstream genome assembly and mapping.

Key Features:

• Context-Aware Merging: Employs a context-aware algorithm to merge overlapping forward and reverse paired-end reads and address increased erroneous bases at read ends.
• Accuracy and Robustness: Experimental results report higher accuracy and robustness compared with state-of-the-art paired-end read merging tools.
• Parallel Processing: Implements multithreading to exploit the inherent parallelism of the paired-end read merging task.
• Application Suitability: Suited for high-throughput amplicon sequencing and validated on both simulated and real high-throughput data sets.

Scientific Applications:

• Amplicon sequencing analysis: Produces longer, more accurate merged reads to improve amplicon sequencing analyses.
• Genome assembly: Supplies elongated, higher-fidelity sequences to enhance genome assembly.
• Mapping: Improves read mapping by providing merged reads with greater contiguous sequence.
• Evolutionary studies: Enables more reliable sequence-based analyses used in evolutionary research.
• Pathogen detection: Supports pathogen detection workflows by generating higher-fidelity sequences from amplicon data.
• Biodiversity assessments: Facilitates biodiversity assessment through improved sequence accuracy and length.

Methodology:

Performs context-aware merging of overlapping forward and reverse paired-end reads that accounts for sequence context to mitigate end-of-read errors and is implemented with multithreading for parallel processing.