FLASH is a fast computational tool designed to extend the length of short reads by overlapping paired-end reads from fragment libraries. It improves genome assemblies by merging reads, which increases the accuracy and completeness of genome assemblies. The tool was tested on simulated and real data, showing high reliability in extending reads with minimal errors. FLASH was applied to genome assemblies of Staphylococcus aureus and human chromosome 14, resulting in significantly larger N50 values for contigs and scaffolds. The tool is implemented in C and is freely available as open-source software. FLASH processes paired-end reads by finding the correct overlap and merging them, which enhances the quality of genome assemblies. It is particularly effective in reducing the number of incorrect merges and improving the accuracy of assemblies. FLASH was compared to SHERA, another tool for extending read lengths, and showed superior performance in terms of accuracy and speed. The tool is robust to varying error rates and can be adjusted for different datasets. FLASH is useful for a wide range of applications, including RNA-seq data. However, it may face challenges with short tandem repeats, where merging reads can lead to the collapse of repeat regions. Despite this, FLASH remains a valuable tool for improving genome assemblies by extending short reads.FLASH is a fast computational tool designed to extend the length of short reads by overlapping paired-end reads from fragment libraries. It improves genome assemblies by merging reads, which increases the accuracy and completeness of genome assemblies. The tool was tested on simulated and real data, showing high reliability in extending reads with minimal errors. FLASH was applied to genome assemblies of Staphylococcus aureus and human chromosome 14, resulting in significantly larger N50 values for contigs and scaffolds. The tool is implemented in C and is freely available as open-source software. FLASH processes paired-end reads by finding the correct overlap and merging them, which enhances the quality of genome assemblies. It is particularly effective in reducing the number of incorrect merges and improving the accuracy of assemblies. FLASH was compared to SHERA, another tool for extending read lengths, and showed superior performance in terms of accuracy and speed. The tool is robust to varying error rates and can be adjusted for different datasets. FLASH is useful for a wide range of applications, including RNA-seq data. However, it may face challenges with short tandem repeats, where merging reads can lead to the collapse of repeat regions. Despite this, FLASH remains a valuable tool for improving genome assemblies by extending short reads.