Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills

The targeted metagenomics study performed by Pollock et al. (Pollock 2018) was part of the Global Coral Microbiome Project (Vega Thurber Lab 2014).  Since the original publication of Pollock et al. (Pollock 2018) was written for a highly specialized academic public, we provided Bsc. students with a short introduction of the paper and guided them through the metadata table stored in the gcmp16S_map_r25.txt file under the GCMP Australia sequence data, OTU tables, and metadata folder (https://doi.org/10.6084/m9.figshare.c.3855466.v2).

In order to process the fastq-files and obtain OTU tables, a custom-made pipeline on a Galaxy instance (Galaxy Community) was used. This pipeline contained data analytical tools obtained from the Naturalis Biodiversity Center GitHub environment (https://github.com/naturalis). In order to align with the newest Galaxy best practices, we updated the tools and links to the original as well as the updated GitHub and toolshed versions are included in the references list.

The names of the original raw fastq-files contain many dots which can hamper file-type recognition during downstream analyses in Galaxy. Therefore, prior to distributing the fastq-files to the students, these names were renamed using the ManageZIP tool (The BLFS Development Team 1999-2023). Dots were replaced with underscores, with an exception made for the last 2 file type extension dots. For example, the file name E1.2.Tur.pelt.1.20140814.M_S71_L001_R1_001.fastq.gz was changed into E1_2_Tur_pelt_1_20140814_M_S71_L001_R1_001_1.fastq.gz. Similarly, the filenames in the metadata table were adjusted accordingly. The total collection of renamed file names is available through this zenodo repository as wel as the accompanying metadata file.