An interactive species classification instrument with educational purposes using NanoDJ and PCR-free mtDNA enrichment
Date:
November 14-16, 2018. Co-authored with Hernández-Beeftink T, Rodríguez-Pérez H, Gonzalez Navasa C, Roda-García JL, Pérez-González CJ, Lorenzo-Salazar JM, González-Montelongo R and Flores C. Abstract Booklet #34, page 52.
Abstract
We have developed NanoDJ, an interactive collection of Jupyter notebooks distributed as a Docker software container, to facilitate Oxford Nanopore Technologies (ONT) sequence analyses by integrating capabilities for data manipulation, sequence comparison and assembly for research and educational purposes. It includes base calling, read filtering, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly. In this study, we show the utility of NanoDJ for the development of a hands‐on genomics educational tool applying mitochondrial DNA (mtDNA) PCR‐free enrichment for species apportionment of food components. After assessing two distinct mtDNA enrichment protocols to pick the best‐performing solution, we used a simple 10‐minute library preparation (SQK‐RAD004) of a mock mixture and a 48‐h MinION (ONT) run obtaining 35,424 reads of 3.5 Kbase mean size. NanoDJ allowed a fast BLAST‐based identification of all species in the sample, thus validating this hand‐on experience as a learning‐by‐doing instrument for transdisciplinary education adapted to basic laboratory resource settings. In conclusion, this instrument can be used as a routine tool for training and education, as well as for research, contributing to democratize the access to the latest advances in genomics. Software availability: https://github.com/genomicsITER/NanoDJ
Funded by Instituto de Salud Carlos III (PI14/00844; FI17/00177) and Ministerio de Ciencia, Innovación y Universidades (RTC‐2017‐6471‐1; MINECO/AEI/FEDER, UE) co‐financed by the European Regional Development Funds, “A way of making Europe” from the European Union; by the agreement OA17/008 with Instituto Tecnológico y de Energías Renovables (ITER) to strengthen scientific and technological education, training, research, development and innovation in Genomics, Personalized Medicine and Biotechnology; and by the CEDeI program (Centro de Excelencia de Desarrollo e Innovación, Cabildo de Tenerife).