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

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 revolutiona...

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Autores principales: Risse, Judith, Thomson, Marian, Patrick, Sheila, Blakely, Garry, Koutsovoulos, Georgios, Blaxter, Mark, Watson, Mick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670535/
https://www.ncbi.nlm.nih.gov/pubmed/26640692
http://dx.doi.org/10.1186/s13742-015-0101-6
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author Risse, Judith
Thomson, Marian
Patrick, Sheila
Blakely, Garry
Koutsovoulos, Georgios
Blaxter, Mark
Watson, Mick
author_facet Risse, Judith
Thomson, Marian
Patrick, Sheila
Blakely, Garry
Koutsovoulos, Georgios
Blaxter, Mark
Watson, Mick
author_sort Risse, Judith
collection PubMed
description 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.
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spelling pubmed-46705352015-12-06 A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data Risse, Judith Thomson, Marian Patrick, Sheila Blakely, Garry Koutsovoulos, Georgios Blaxter, Mark Watson, Mick Gigascience Data Note 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. BioMed Central 2015-12-04 /pmc/articles/PMC4670535/ /pubmed/26640692 http://dx.doi.org/10.1186/s13742-015-0101-6 Text en © Risse et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Data Note
Risse, Judith
Thomson, Marian
Patrick, Sheila
Blakely, Garry
Koutsovoulos, Georgios
Blaxter, Mark
Watson, Mick
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
title A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
title_full A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
title_fullStr A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
title_full_unstemmed A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
title_short A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
title_sort single chromosome assembly of bacteroides fragilis strain be1 from illumina and minion nanopore sequencing data
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670535/
https://www.ncbi.nlm.nih.gov/pubmed/26640692
http://dx.doi.org/10.1186/s13742-015-0101-6
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