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  Tamara Hernández-Beeftink³  Héctor Rodríguez-Pérez³  Carlos Flores⁴  José M. Lorenzo-Salazar⁵ 

[1] 0000000121060879, grid.10041.34, Departamento de Ingeniería Informática y de Sistemas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain;0000000121060879, grid.10041.34, Departamento de Matemáticas, Estadística e Investigación Operativa, Universidad de La Laguna, Santa Cruz de Tenerife, Spain;0000000121060879, grid.10041.34, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain;0000000121060879, grid.10041.34, Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain;grid.425233.1, Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain;0000 0000 9314 1427, grid.413448.e, CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain;grid.425233.1, Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain;

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

DOI  :  10.1186/s12859-019-2860-z

来源: publisher

【 摘 要 】

BackgroundThe 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 procedures 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.

【 授权许可】

CC BY