CASPER

CASPER is a software tool used in bioinformatics to improve the performance of downstream tasks like genome assembly and mapping by merging forward and reverse reads from paired-end sequencing. This process helps provide longer, more accurate reads to these tasks. However, the tool faces challenges due to the limitations of most paired-end sequencers, where the chances of observing erroneous bases increase as the end of a read is approached. Despite the existence of other methods to solve this problem, their performance remains unsatisfactory. CASPER addresses this issue through a context-aware scheme that quickly and reliably merges overlapping paired-end reads. It performs better than existing state-of-the-art tools in terms of accuracy and robustness. Additionally, it utilizes parallelism to speed up the process of paired-end merging. CASPER is freely available for academic use at its website.