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

From: Clinical detection and characterization of bacterial pathogens in the genomics era

Sequencing technology Platform Mb/runa 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
Roche (454) GS Junior 35 4 hours 250
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
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
MinION
  1. aAbbreviations: NA, data not available.