ls, cd, head, wc … See Astrobiomike’s tutorial
Ability to install packages and create/activate environments using conda (or modern alternatives such as mamba or micromamba)
for loops, using Bash variables (like $REFERENCE). See this short tutorial.“Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analysis” (2020) This relatively recent review offers a detailed introduction to metagenomics with a strong emphasis on analysis pipelines for both whole-genome and marker gene data, covering best practices, comparisons of tools, and guidelines
“Introduction to Metagenomics: Tools, Workflows & Insights” (2025, Blog) A good blog post with a broad overview that bridges conceptual foundations with practical workflows, describing sequencing technologies, data analysis strategies, and examples of ecological discoveries
“Genome-resolved metagenomics: a game changer for microbiome studies” (2024)
This review explains the transition from traditional methods to genome-resolved metagenomics, highlighting its impact on human microbiome research with approachable explanations for students.
“Metagenomics: An Effective Approach for Exploring Microbial Diversity” (2023) Focused on applications in human microbiome research, this review is easy to follow and discusses technological advances, pipelines, and key databases relevant for analysis.
A practical guide to amplicon and metagenomic analysis of microbiome data (2024) This guide shows how 16S (amplicon) and metagenomics workflow produce their data and how they can be integrated with downstream analyses