A method for preparing nucleic acid molecules from a biological sample comprising the steps of: delivering the biological sample to a disposable cartridge with a cylindrical reservoir insert having a plurality of chambers including a first chamber with a first port that terminates at an outer wall of the cylindrical reservoir insert, the cylindrical reservoir insert being rotatable about an axis of rotation and the outer wall being parallel to the axis of rotation and defining a perimeter of the cylindrical reservoir insert, the plurality of chambers being within the perimeter of the outer wall, a through-channel that extends along a bottom surface of the cylindrical reservoir insert, the through-channel having a second port and a third port at respective ends of the through-channel and each terminating at the outer wall; mixing said biological sample in a first volume of buffer to said first chamber; fragmenting said sample in the presence of 0.1-10% of a size stabilizer, selected from a detergent, surfactant, soap, and a chaotropic salt, to obtain the nucleic acid molecules; attaching said nucleic acid molecules to magnetic nanoparticles and subsequently applying a magnetic field to concentrate said magnetic nanoparticles and any nucleic acid molecules attached thereto to a first portion of a first reservoir in said disposable cartridge; aligning the first port with a plunger; actuating the plunger to withdraw the nucleic acid molecules out of the disposable cartridge and into the plunger; aligning the second port with the plunger by rotating the cylindrical reservoir insert about the axis of rotation; and actuating the plunger to inject the nucleic acid molecules out of the plunger and into the through-channel. delivering the biological sample to a disposable cartridge with a cylindrical reservoir insert having a plurality of chambers including a first chamber with a first port that terminates at an outer wall of the cylindrical reservoir insert, the cylindrical reservoir insert being rotatable about an axis of rotation and the outer wall being parallel to the axis of rotation and defining a perimeter of the cylindrical reservoir insert, the plurality of chambers being within the perimeter of the outer wall, a through-channel that extends along a bottom surface of the cylindrical reservoir insert, the through-channel having a second port and a third port at respective ends of the through-channel and each terminating at the outer wall; mixing said biological sample in a first volume of buffer to said first chamber; fragmenting said sample in the presence of 0.1-10% of a size stabilizer, selected from a detergent, surfactant, soap, and a chaotropic salt, to obtain the nucleic acid molecules; attaching said nucleic acid molecules to magnetic nanoparticles and subsequently applying a magnetic field to concentrate said magnetic nanoparticles and any nucleic acid molecules attached thereto to a first portion of a first reservoir in said disposable cartridge; aligning the first port with a plunger; actuating the plunger to withdraw the nucleic acid molecules out of the disposable cartridge and into the plunger; aligning the second port with the plunger by rotating the cylindrical reservoir insert about the axis of rotation; and actuating the plunger to inject the nucleic acid molecules out of the plunger and into the through-channel.