The paper introduces GapFiller, an automated strategy for closing gaps within scaffolds using paired reads in de novo genome assemblies. The method is designed to reduce the need for additional wet-lab work, such as Sanger sequencing, which is often required to close incomplete regions. GapFiller is evaluated on both bacterial and eukaryotic datasets, showing promising results with fewer errors and a significant reduction in gap length compared to other methods like IMAGE and SOAPdenovo. The software is user-friendly and efficient, requiring limited computational resources. Functional analysis of the closed regions in the human genome reveals that they contain important coding and non-coding information. GapFiller is particularly effective in closing gaps in repetitive and low-coverage regions, making it a valuable tool for improving the accuracy of genome assemblies.The paper introduces GapFiller, an automated strategy for closing gaps within scaffolds using paired reads in de novo genome assemblies. The method is designed to reduce the need for additional wet-lab work, such as Sanger sequencing, which is often required to close incomplete regions. GapFiller is evaluated on both bacterial and eukaryotic datasets, showing promising results with fewer errors and a significant reduction in gap length compared to other methods like IMAGE and SOAPdenovo. The software is user-friendly and efficient, requiring limited computational resources. Functional analysis of the closed regions in the human genome reveals that they contain important coding and non-coding information. GapFiller is particularly effective in closing gaps in repetitive and low-coverage regions, making it a valuable tool for improving the accuracy of genome assemblies.