2 Base Encoding - Disadvantages

Disadvantages

When base calling single color miscalls cause errors on the remaining portion of the read. In SNP calling this can be corrected, which results in a lower SNP calling error rate. However for simplistic de novo assembly you are left with the raw device error rate which will be significantly higher than the 0.06% reported for SNP calling. Quality filtering of the reads can deliver higher raw accuracy reads which when aligned to form color contigs can deliver reference sequences where 2 base encoding can be better leveraged. Hybrid assemblies with other technologies can also better utilize the 2 base encoding.