Table II.

Technological strategies for assessing satellite DNA

Platform	Read length; method	Pros	Cons	Example
Illumina	Up to 300 bp; clustered amplicon	Inexpensive, low error rate	PCR bias in library prep*; short reads	[40]
Ion torrent	Up to 400 bp; on-bead amplicon	Fast, inexpensive	Lower yield; high error rate in homopolymer tracts	[27]
Pacific Biosciences	Up to 50 kb; single molecule	Long reads; can assemble complex satellite regions	Expensive; high error rate**	[5]
Oxford Nanopore	Up to 300 kb; single molecule	Longest reads	High error rate; extracting high molecular weight DNA is limiting	Jain et al., bioRxiv 10.1101/170373
Optical mapping (nanochannel)	Up to 220 kb; single molecule	Long-range positional information; orthogonal method to sequencing	Requires a reference genome; large nicking intervals preclude mapping simple sequences	[41]

^*PCR-free libraries reduce bias.

^**PacBio also offers a Circular Consensus Sequencing (CSS) approach, where single circular molecules are read multiple times, thus generating a high quality consensus for each molecule.