Type: Article

A Data Carpentry- Style Metagenomics Workshop

Claudia Zirión-Martínez; Diego Garfias-Gallegos; Tania Vanessa Arellano-Fernandez; Aarón Espinosa-Jaime; Edder D Bustos-Díaz; José Abel Lovaco-Flores; Luis Gerardo Tejero-Gómez; J Abraham Avelar-Rivas; Nelly Sélem-Mojica;

Abstract:

Metagenomic analyses aim to explore the genomic diversity of communities in specific habitats by processing their DNA sequencing data. This analysis is achieved with special- ized bioinformatics tools, which often require previous coding experience. Furthermore, beginners can struggle to build a pipeline from raw data to valuable biological insights. The Carpentries hosts open lessons used worldwide to analyze specialized datasets for beginners, including a Data Carpentry curriculum for individuals working with genomics sequencing data. However, a lesson addressing the specific challenges associated with metagenomics data and analyses was missing. We created a complete Metagenomics curriculum in The Carpentries Incubator, adapting and expanding on the Data Carpentry Metagenomics curriculum. The curriculum provides an introduction to programming, teaching learners to access and handle metagenomics data, and to run commands with the software needed for completing metagenomics analyses. Content and exercises have been improved based on experience gathered in teaching the curriculum in three 16-hour online workshops. We expect to continue to enhance this lesson, which we hope is helpful as a teaching resource for new instructors in the field, and as a guide for newcomers wishing to perform metagenomic analyses from scratch.