Clinical detection and characterization of bacterial pathogens in the genomics era

Table 1 Technology, platforms and features of the currently available sequencing methods

Sequencing technology	Platform	Mb/run^a	Time/run	Read length (bp)	Limits	Applications
Sanger di-deoxy nucleotide sequencing	Capillary sequencers, for example, Life Technologies ABI3730	0.44	7 hours	650-800	Cost, need for high DNA amounts, cloning step	De novo sequencing
Pyrosequencing	Roche (454) GS-FLX	700	24 hours	700	Difficulty in disambiguating repeat regions, misincorporation of excess nucleotides	De novo sequencing
Pyrosequencing	Roche (454) GS Junior	35	4 hours	250		De novo sequencing
Sequencing by synthesis	Illumina Genome Analyzer II	95 × 10³	14 days	2 × 150	Limited paired-end and targeted sequencing	Resequencing
	Illumina Hi Seq2500	6 × 10⁵	11 days	2 × 100		Resequencing
	Illumina MiSeq	15 × 10³	56 hours	2 × 300		De novo sequencing, resequencing
Ligation-based sequencing	Life Technologies SOLID 5500	32 × 10³	15 days	50 + 35	Specific sequence format, difficult sequence assembly	Resequencing
Semiconductor sequencing	Ion Torrent PGM	200	4 hours	200-400	Artificial insertions or deletions in mononucleotide repeats	Resequencing
	Ion Torrent Proton	2.5 × 10³	4 hours	100-200		Resequencing
	Ion Torrent Proton	2.5 × 10³	4 hours	100-200		Resequencing
SMRT technology	Pacific Biosciences PacBio RSII	0.5-1 × 10³	4 hours	10³-10⁴	Substitution errors	De novo sequencing and genome structure
Ionic current sensing	Oxford Nanopore Technologies	NA	No fixed run-time	10⁴-5 × 10⁴	NA	De novo sequencing
Ionic current sensing	MinION	NA	No fixed run-time	10⁴-5 × 10⁴	NA	De novo sequencing

ISSN: 1756-994X