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

Rodriguez-Perez, H.; Tamara, H.-B.; Lorenzo-Salazar, J. M.; Roda-Garcia, J. L.; Perez-Gonzalez, C. J.; Colebrook, M.; Flores, C.

doi:10.1101/586842

bioRxiv · 10.1101/586842

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

Rodriguez-Perez, H.·Tamara, H.-B.·Lorenzo-Salazar, J. M.·Roda-Garcia, J. L.·Perez-Gonzalez, C. J.·Colebrook, M.·Flores, C.

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Abstract

BackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.\n\nResultsWe 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.\n\nConclusionsWith 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.

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Rodriguez-Perez, H., Tamara, H.-B., Lorenzo-Salazar, J. M., Roda-Garcia, J. L., Perez-Gonzalez, C. J., Colebrook, M., Flores, C.. 2019-03-28. NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly. https://doi.org/10.1101/586842

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