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

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 234 - 4
• Main Authors: Rodríguez-Pérez, Héctor, Hernández-Beeftink, Tamara, Lorenzo-Salazar, José M., Roda-García, José L., Pérez-González, Carlos J., Colebrook, Marcos, Flores, Carlos
• Format: Journal Article
• Language: English
• Published: London BioMed Central 09.05.2019; BioMed Central Ltd; BMC
• Subjects: Algorithms; Assembly; Base sequence; Bioinformatics; Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Deoxyribonucleic acid; DNA; DNA sequencing; Docker; Educational technology; Gene sequencing; Genome analysis; Genomes; Genomics; Jupyter; Life Sciences; Methods; Microarrays; Nanopore sequencing; Nanotechnology; Nucleotide sequence; Open source software; Porosity; Quality control; Sequence analysis (methods); Software; Study and teaching; Technology; Visualization (Computer); Web applications; Spain; Jupyter; Genome analysis; Docker; Nanopore sequencing
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2860-z

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 .