SUMMARY: Linked genomic sequencing reads contain information that can be used to join sequences together into scaffolds in draft genome assemblies. Existing software for this purpose performs the scaffolding by joining sequences with a gap between them, not considering potential overlaps of contigs. We developed ARBitR to create scaffolds where overlaps are taken into account and show that it can accurately recreate regions where draft assemblies are broken. AVAILABILITY AND IMPLEMENTATION: ARBitR is written and implemented in Python3 for Unix-based operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License v3. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.