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A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

Judith Risse, Marian Thomson, Garry Blakely, Georgios Koutsovoulos, Mark Blaxter, Mick Watson
doi: https://doi.org/10.1101/024323
Judith Risse
1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL
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Marian Thomson
1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL
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Garry Blakely
2Institute of Cell Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3BF
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Georgios Koutsovoulos
3Institute of Evolutionary Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL
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Mark Blaxter
1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL
3Institute of Evolutionary Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL
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Mick Watson
1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL
4The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG
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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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted August 11, 2015.
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A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
Judith Risse, Marian Thomson, Garry Blakely, Georgios Koutsovoulos, Mark Blaxter, Mick Watson
bioRxiv 024323; doi: https://doi.org/10.1101/024323
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A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
Judith Risse, Marian Thomson, Garry Blakely, Georgios Koutsovoulos, Mark Blaxter, Mick Watson
bioRxiv 024323; doi: https://doi.org/10.1101/024323

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