The advances in next-generation sequencing technology (NGS) have triggered a variety of active biological studies across multiple disciplines. The sequencing technology by Illumina is one of the most widely used methods despite the relatively short reads length and high error rates compared to other NGS technologies. These disadvantages can be alleviated by producing paired-end reads and merging them. By merging the ends of both reads, the error rate can be reduced, and the reads can be effectively elongated. In this paper, we compare three paired-end merging methods (COPE, FLASH, PANDAseq) and carry out comparative studies on their effectiveness on a public 16S rRNA sequencing dataset.