Helicos Single-Molecule Sequencing of Bacterial Genomes

  • Kathleen E. SteinmannEmail author
  • Christopher E. Hart
  • John F. Thompson
  • Patrice M. Milos
Part of the Methods in Molecular Biology book series (MIMB, volume 733)


With the advent of high-throughput sequencing technologies, multiple bacterial genomes can be sequenced in days. While the ultimate goal of de novo assembly of bacterial genomes is progressing, changes in the genomic sequence of closely related bacterial strains and isolates are now easily monitored by comparison of their sequences to those of a reference genome. Such studies can be applied to the fields of bacterial evolution, epidemiology, and diagnostics. We present a protocol for single-molecule sequencing of bacterial DNA whose end result is the identification of single nucleotide variants, and various size insertions and deletions relative to a reference genome. The protocol is characterized by the simplicity of sample preparation and the lack of amplification-related sequencing bias.

Key words

Bacterial genome Single-molecule sequencing Sequencing bias SNV PolyA tail HeliScopeTM sequencer 



The authors would like to acknowledge the valuable contributions of Katica Ilic, Kristen Kerouac, and Eldar Giladi.


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Kathleen E. Steinmann
    • 1
    Email author
  • Christopher E. Hart
  • John F. Thompson
  • Patrice M. Milos
  1. 1.Helicos BioSciences CorporationCambridgeUSA

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