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Title: Supporting data for "The use of Oxford Nanopore native barcoding for complete genome assembly"      
dateReleased:
12-31-2016
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
12-31-2016
refinement:
curated
ID:
doi:10.5524/100269
creators:
Bayliss, Sion C
Hunt, Vicky L
Yokoyama, Maho
Thorpe, Harry A
Feil, Edward J
availability:
available
types:
sequence
description:
The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data. The strain we used, MHO_001, represents the important community-acquired methicillin resistant Staphylococcus aureus lineage USA300. Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The longread data represented only ~5-10% of an average MinION(TM) run (~7x genomic coverage) but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss and gain of mobile genetic elements. Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short-read data, to fully complete a bacterial genome. The ability to complete multiple genomes, for which short-read data is already available, from a single MinION(TM) run is set to impact on our understanding of accessory genome content, plasmid diversity and genome rearrangements.
accessURL: https://doi.org/10.5524/100269
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

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