Embodiments of systems and methods for automated sample handling are disclosed. In an example, a system for automated sample handling includes reaction wells, a magnet, a magnetic manipulator, and a punch. The reaction wells are configured to each hold a reagent and collectively move horizontally. A first reaction well holds magnetic beads, and a second reaction well is partitioned by a seal. The magnet is configured to move vertically and capture the magnetic beads on a bottom surface of the first reaction well when moving to an upper position beneath the first reaction well. The magnetic manipulator is configured to manipulate the magnetic beads and includes a magnetic rod configured to move vertically to be above or in the first reaction well and a sheath below the magnetic rod and configured to move vertically and receive the magnetic rod. The punch is configured to move vertically and break the seal of the second reaction well when moving to a lower position in the second reaction well.