BBMerge is a new tool for accurately merging paired-end shotgun reads using overlap. It improves accuracy and reduces processing time, allowing the use of read merging on larger datasets. The tool was benchmarked against eight other widely used merging tools, showing superior performance in accuracy and speed. BBMerge can merge non-overlapping read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy. The tool was tested on synthetic and real-world datasets, including a eukaryotic genome and a microbial community. BBMerge's performance was evaluated based on accuracy, speed, and scalability. It outperformed other tools in merging accuracy, with the lowest rate of incorrectly merged reads. BBMerge also showed excellent scalability, with near-perfect scaling in multi-threaded environments. Assembly quality was evaluated using QUAST, showing improved assembly continuity and reduced misassemblies. BBMerge variants, such as REM and RSEM, achieved higher accuracy and merge rates compared to other tools. The tool is designed for production use and supports a wide variety of input and output formats. It is written in Java and can be deployed on any computer supporting Java. BBMerge is a promising tool for improving the assembly of large datasets such as shotgun metagenomes.BBMerge is a new tool for accurately merging paired-end shotgun reads using overlap. It improves accuracy and reduces processing time, allowing the use of read merging on larger datasets. The tool was benchmarked against eight other widely used merging tools, showing superior performance in accuracy and speed. BBMerge can merge non-overlapping read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy. The tool was tested on synthetic and real-world datasets, including a eukaryotic genome and a microbial community. BBMerge's performance was evaluated based on accuracy, speed, and scalability. It outperformed other tools in merging accuracy, with the lowest rate of incorrectly merged reads. BBMerge also showed excellent scalability, with near-perfect scaling in multi-threaded environments. Assembly quality was evaluated using QUAST, showing improved assembly continuity and reduced misassemblies. BBMerge variants, such as REM and RSEM, achieved higher accuracy and merge rates compared to other tools. The tool is designed for production use and supports a wide variety of input and output formats. It is written in Java and can be deployed on any computer supporting Java. BBMerge is a promising tool for improving the assembly of large datasets such as shotgun metagenomes.