*5.5. Sequencing*

Following amplification of DNA, the sequencing strategy used is dependent on a variety of factors including the choice of marker, with most studies thus far utilising the Illumina MiSeq platform. Although concerns are raised over the maximum read length of Illumina platforms (2 × 300 bp) [29,98], multiple studies have demonstrated successful sequencing of longer markers such as *rbcL* (around 500 bp) along with additional adapters and primers [45,80]. Newer sequencing technologies such as the MinION (Oxford Nanopore Technologies) and SMRT platform (PACBIO, Pacific Biosciences) produce longer read lengths, but they generate less reads than Illumina [29]. The development of ultra-deep short read sequencing technologies such as Illumina NovaSeq provide an opportunity to increase sequencing depth and improve the detection rate of taxa. The requirement for high quality and quantity of input DNA may be a limiting factor for some applications of these technologies [49].
