BBMerge is a new tool designed for merging paired-end shotgun reads to improve subsequent bioinformatics processes such as genome assembly, binning, mapping, annotation, and clustering. The tool aims to maximize accuracy and minimize processing time, making it suitable for large datasets and sensitive analyses. BBMerge is benchmarked against eight other widely used merging tools, demonstrating superior performance in terms of speed, accuracy, and scalability. BBMerge can handle non-overlapping pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a higher merge rate while maintaining or improving accuracy. The tool is written in Java, supports various input and output formats, and is designed for production use, making it a promising tool for improving the assembly of large datasets like shotgun metagenomes.BBMerge is a new tool designed for merging paired-end shotgun reads to improve subsequent bioinformatics processes such as genome assembly, binning, mapping, annotation, and clustering. The tool aims to maximize accuracy and minimize processing time, making it suitable for large datasets and sensitive analyses. BBMerge is benchmarked against eight other widely used merging tools, demonstrating superior performance in terms of speed, accuracy, and scalability. BBMerge can handle non-overlapping pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a higher merge rate while maintaining or improving accuracy. The tool is written in Java, supports various input and output formats, and is designed for production use, making it a promising tool for improving the assembly of large datasets like shotgun metagenomes.