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

BMC Bioinformatics

José L. Roda-García¹  Marcos Colebrook¹  Carlos J. Pérez-González²  José M. Lorenzo-Salazar³  Carlos Flores⁴  Héctor Rodríguez-Pérez⁴  Tamara Hernández-Beeftink⁴ 

[1] Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna;Departamento de Matemáticas, Estadística e Investigación Operativa, Universidad de La Laguna;Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER);Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna;

关键词: Genome analysis;    Nanopore sequencing;    Jupyter;    Docker;   

DOI  :  10.1186/s12859-019-2860-z

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown