title: A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data.
abstract: BACKGROUND
  Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes. The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.
  
  
  RESULTS
  We sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms. We were able to assemble a single chromosome of 5.18 Mb, with no gaps, using publicly available software and commodity computing hardware. We identified gene rearrangements and the state of invertible promoters in the strain.
  
  
  CONCLUSIONS
  The single chromosome assembly of Bacteroides fragilis strain BE1 was achieved using only modest amounts of data, publicly available software and commodity computing hardware. This combination of technologies offers the possibility of ultra-cheap, high quality, finished bacterial genomes.
authors.affiliation: Edinburgh Genomics, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3FL Edinburgh, UK.
authors.forename: Judith
authors.initials: J
authors.lastname: Risse
authors.affiliation: Edinburgh Genomics, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3FL Edinburgh, UK.
authors.forename: Marian
authors.initials: M
authors.lastname: Thomson
authors.affiliation: Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.
authors.forename: Sheila
authors.initials: S
authors.lastname: Patrick
authors.affiliation: Institute of Cell Biology, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3BF Edinburgh, UK.
authors.forename: Garry
authors.initials: G
authors.lastname: Blakely
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3FL Edinburgh, UK.
authors.forename: Georgios
authors.initials: G
authors.lastname: Koutsovoulos
authors.affiliation: Edinburgh Genomics, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3FL Edinburgh, UK ; Institute of Evolutionary Biology, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3FL Edinburgh, UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Blaxter
authors.affiliation: Edinburgh Genomics, School of Biological Sciences, The King's Buildings, The University of Edinburgh, EH9 3FL Edinburgh, UK ; The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, UK.
authors.forename: Mick
authors.initials: M
authors.lastname: Watson
mesh_terms: D001441:Bacteroides fragilis / Q000235:genetics*; D002876:Chromosomes, Bacterial; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software