Results: The data generated was largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (p = 0.371) and average sequence length (p = 0718) of endogenous nuclear DNA, sequence GC content (p = 0.311), double stranded DNA damage rate (p = 0.309), and sequence clonality (p = 0.093). Small significant differences were found in single strand DNA damage rate (δS, slight lower for the BGISEQ-500, p = 0.011) and the background rate of difference from the reference genome (θ, slightly higher for BGISEQ-500, p = 0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (p = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA.
Conclusions: Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
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- Ancient DNA
- Illumina HiSeq 2500
- Comparative performance