Table 1.

Comparison of next-generation sequencing technologies adapted from Metzker (2010)

Platform	Library preparation	Chemistry	Consensus accuracy	Average read length (bp)	Reads per run	Run time	Pros	Cons	Application	References
Roche 454 GS FLX Titanium+	Fragment, Mate Pair/ emPCR	Pyrosequencing	99.997%	~700, maximum 1000	~1,000,000	23 h	Long read length	High reagent cost, homopolymer repeat errors	De novo assemblies, metagenomics	http://454.com/products/gs-flx-system/index.asp
Illumina- Solexa MiSeq	Fragment, Mate Pair/ Solid phase	Reversible terminator	98%	2 × 300	~25,000,000	~55 h 300 bp reads	Widely used platform	Short read length	Small genomes, 16s amplicon, improving coverage	http://systems.illumina.com/systems/miseq.html
Life Technologies SOLiD 5500 Series	Fragment, Mate Pair/ emPCR	Sequencing by ligation (Cleavable probe)	99.99%	Mate-paired 2 × 60, Paired-end 75 × 35 Fragment 75	1.2–1.4 billion	1–2 weeks	Low-cost	Slow, issues with palindromic sequences reported	Whole genome re-sequencing, variant analysis	http://www.lifetechnologies.com/ (Huang et al. 2012)
Life Technologies Ion Torrent	Fragment, Mate Pair/ emPCR	Sequential ion detection	98%	35–400	80,000,000	90 min	Fast and inexpensive	Reported homopolymer errors	Small genomes, gene expression, ChiP-SEQ	http://www.lifetechnologies.com/
Pacific Biosciences SMRT RS II	Fragment only/ Single molecule	Real-time	99.999%	N50 14,000, maximum >40,000	~50,000	30 min–4 h	Longest read length, detects base modifications, fast	Low single sequence accuracy 87%	De novo assemblies, Base modification detection, Transcriptome sequencing	(Murray et al. 2012; Chin et al. 2013) http://www.pacificbiosciences.com/