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

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 sequenc...

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Autores principales: Rodríguez-Pérez, Héctor, Hernández-Beeftink, Tamara, Lorenzo-Salazar, José M., Roda-García, José L., Pérez-González, Carlos J., Colebrook, Marcos, Flores, Carlos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509807/
https://www.ncbi.nlm.nih.gov/pubmed/31072312
http://dx.doi.org/10.1186/s12859-019-2860-z
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author Rodríguez-Pérez, Héctor
Hernández-Beeftink, Tamara
Lorenzo-Salazar, José M.
Roda-García, José L.
Pérez-González, Carlos J.
Colebrook, Marcos
Flores, Carlos
author_facet Rodríguez-Pérez, Héctor
Hernández-Beeftink, Tamara
Lorenzo-Salazar, José M.
Roda-García, José L.
Pérez-González, Carlos J.
Colebrook, Marcos
Flores, Carlos
author_sort Rodríguez-Pérez, Héctor
collection PubMed
description 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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spelling pubmed-65098072019-06-05 NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly Rodríguez-Pérez, Héctor Hernández-Beeftink, Tamara Lorenzo-Salazar, José M. Roda-García, José L. Pérez-González, Carlos J. Colebrook, Marcos Flores, Carlos BMC Bioinformatics Software 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. BioMed Central 2019-05-09 /pmc/articles/PMC6509807/ /pubmed/31072312 http://dx.doi.org/10.1186/s12859-019-2860-z Text en © The Author(s). 2019 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 Software
Rodríguez-Pérez, Héctor
Hernández-Beeftink, Tamara
Lorenzo-Salazar, José M.
Roda-García, José L.
Pérez-González, Carlos J.
Colebrook, Marcos
Flores, Carlos
NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
title NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
title_full NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
title_fullStr NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
title_full_unstemmed NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
title_short NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
title_sort nanodj: a dockerized jupyter notebook for interactive oxford nanopore minion sequence manipulation and genome assembly
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509807/
https://www.ncbi.nlm.nih.gov/pubmed/31072312
http://dx.doi.org/10.1186/s12859-019-2860-z
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