NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly [article]

Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores
2019 bioRxiv   pre-print
AbstractBackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.ResultsWe 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
more » ... s for hybrid assembly.ConclusionsWith 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.
doi:10.1101/586842 fatcat:2vyy2smntvavnpj3lvuud2fngy