NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly

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Abstract

Background

The Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.

Results

We present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly.

Conclusions

With the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aimed to simplify and make more reproducible ONT DNA sequence analysis. The NanoDJ package code, documentation and installation instructions are freely available at https://github.com/genomicsITER/NanoDJ.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2860-z) contains supplementary material, which is available to authorized users.

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Most cited references 8

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Completing bacterial genome assemblies with multiplex MinION sequencing

Ryan Wick, Louise Judd, Claire Gorrie … (2017)

Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read length limits its ability to resolve genomic structure. This has major implications for tracking the spread of mobile genetic elements, including those which carry antimicrobial resistance determinants. Fully resolving a bacterial genome requires long-read sequencing such as those generated by Oxford Nanopore Technologies (ONT) platforms. Here we describe our use of the ONT MinION to sequence 12 isolates of Klebsiella pneumoniae on a single flow cell. We assembled each genome using a combination of ONT reads and previously available Illumina reads, and little to no manual intervention was needed to achieve fully resolved assemblies using the Unicycler hybrid assembler. Assembling only ONT reads with Canu was less effective, resulting in fewer resolved genomes and higher error rates even following error correction with Nanopolish. We demonstrate that multiplexed ONT sequencing is a valuable tool for high-throughput bacterial genome finishing. Specifically, we advocate the use of Illumina sequencing as a first analysis step, followed by ONT reads as needed to resolve genomic structure.

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An introduction to Docker for reproducible research

Carl Boettiger (2015)

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Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer.

Sarah S Johnson, Elena Zaikova, David Goerlitz … (2017)

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions.

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Author and article information

Contributors

Marcos Colebrook: mcolesan@ull.edu.es

Carlos Flores:

ORCID: http://orcid.org/0000-0001-5352-069X

cflores@ull.edu.es

Journal

Journal ID (nlm-ta): BMC Bioinformatics

Journal ID (iso-abbrev): BMC Bioinformatics

Title: BMC Bioinformatics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2105

Publication date (Electronic): 9 May 2019

Publication date PMC-release: 9 May 2019

Publication date Collection: 2019

Volume: 20

Electronic Location Identifier: 234

Affiliations

[1 ]ISNI 0000000121060879, GRID grid.10041.34, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, , Universidad de La Laguna, ; Santa Cruz de Tenerife, Spain

[2 ]GRID grid.425233.1, Genomics Division, , Instituto Tecnológico y de Energías Renovables (ITER), ; Santa Cruz de Tenerife, Spain

[3 ]ISNI 0000000121060879, GRID grid.10041.34, Departamento de Ingeniería Informática y de Sistemas, , Universidad de La Laguna, ; Santa Cruz de Tenerife, Spain

[4 ]ISNI 0000000121060879, GRID grid.10041.34, Departamento de Matemáticas, Estadística e Investigación Operativa, , Universidad de La Laguna, ; Santa Cruz de Tenerife, Spain

[5 ]ISNI 0000 0000 9314 1427, GRID grid.413448.e, CIBER de Enfermedades Respiratorias, , Instituto de Salud Carlos III, ; Madrid, Spain

Author information

Carlos Flores http://orcid.org/0000-0001-5352-069X

Article

Publisher ID: 2860

DOI: 10.1186/s12859-019-2860-z

PMC ID: 6509807

PubMed ID: 31072312

SO-VID: 1736edb3-54af-41f1-89d3-2deca5076385

License:

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.

History

Date received : 22 June 2018

Date accepted : 29 April 2019

Funding

Funded by: Spanish Ministry of Economy and Competitiveness

Award ID: MTM2016-74877-P

Award Recipient : Marcos Colebrook

Funded by: Instituto de Salud Carlos III rom the Spanish Ministry of Economy and Competitiveness, co-financed by the European Regional Development Funds ‘A way of making Europe’ from the European Union

Award ID: PI14/00844

Award ID: PI17/00610

Award Recipient : Carlos Flores

Funded by: Agreement with Instituto Tecnológico y de Energías Renovables (ITER) to strengthen scientific and technological education, training, research, development and innovation in Genomics, Personalized Medicine and Biotechnology

Award ID: OA17/008

Award Recipient : Carlos Flores

Funded by: Spanish Ministry of Science, Innovation and Universities

Award ID: RTC-2017-6471-1

Award Recipient : Carlos Flores

Funded by: Area Tenerife 2030, Cabildo de Tenerife

Award ID: CGIEU0000219140

Award Recipient : Carlos Flores

Custom metadata

ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: genome analysis,nanopore sequencing,jupyter,docker

Data availability:

ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: genome analysis, nanopore sequencing, jupyter, docker

NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly

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Electronic supplementary material

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Genetoberfest

Most cited references 8

Completing bacterial genome assemblies with multiplex MinION sequencing

An introduction to Docker for reproducible research

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer.

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