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

Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores
2019 BMC Bioinformatics  
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
more » ... sembly. 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
doi:10.1186/s12859-019-2860-z fatcat:4pliw7jdanfjrlqsn65vpfpqo4