Peste-des-petit-ruminants virus is currently the focus of a control and eradication program launched by the FAO and OIE. One of the important steps in the control strategy is strengthening the laboratory capacity and improve molecular methods to characterize field isolates. This protocol describes the preparation of samples for sequencing using the MinION sequencer, from cDNA synthesis, PCR amplification using multiplex primers to loading off the sample on the flow cell. The miniPCR is used as the thermo cycler, making this protocol fully field-adapted and ready to use in the field or in a less well-equipped lab.