Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms. In this study, we analyzed NGS data of virus rescued from a CSFV C-strain vaccine strain cDNA clone. The virus analyzed was obtained from a 4th and a 12th passage of rescued virus in SFT cell culture, which had shown a difference in growth kinetics between the passages, and NGS analysis was chosen in order to look for molecular differences. Identical RT-PCR products were run on both GS FLX and an Iontorrent PGM platform for comparison. The NGS data was compared by quality and the percentage mapped reads. Results showed good quality of reads for both platforms and a close to 100% of the reads mapped to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D3431G in the RNAdependent RNA polymerase NS5B. This SNV was present at 100% frequency in the 12th passage and only at 55% in the 4th passage, which could explain the difference in growth kinetics between the passages.