Methods, devices, systems, and kits useful for the collection and analysis of samples obtained by swabs are disclosed. Swab containers configured for receiving a swab containing a sample; cartridges for holding one or more of: a swab container, a swab, assay units, pipette tips, vessels, transport units, and implements; systems (which may include a sample processing device); kits; and methods for their use are disclosed. A swab container may include an entry port; an assay chamber having an assay port; a conduit comprising an interior channel connecting the entry port; and an interior channel providing fluidic communication between the entry port and assay chamber. An interior channel may be configured to squeeze a portion of a swab placed in or through the conduit. A cartridge may include a cartridge frame configured to receive one or more of swab containers, assay units, transport units, pipette tips, vessels or implements.