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

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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.

Authors: Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores
BMC Bioinformatics - Full text
  • Published on: May 9 2019

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