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tutorials.yaml
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tutorials.yaml
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- title: An introduction to Unix
type: tutorial
url: https://astrobiomike.github.io/unix/getting-started
authors: [AstrobioMike]
summary: "Basics of the command line environment, the best friend of any scientist who wishes to work with data."
tags: [hands-on, beginner]
- title: Basics of metagenomic read recruitment
type: tutorial
url: https://youtu.be/MqD4aN1p1qA?t=344
authors: [meren]
summary: "A very simple introduction to metagenomic read recruitment."
tags: [metagenomics, theoretical, beginner]
- title: A metagenomic read recruitment exercise
type: tutorial
url: https://merenlab.org/tutorials/read-recruitment/
authors: [meren]
summary: "A mini hands-on exercise is to conduct a simple read recruitment experiment with a mock dataset."
tags: [metagenomics, hands-on, beginner]
- title: The anvi'o pangenomics workflow
type: tutorial
url: https://merenlab.org/2016/11/08/pangenomics-v2/
authors: [meren, ShaiberAlon, mahmoudyousef98, ozcan]
summary: "A comprehensive description of the anvi'o pangenomics workflow."
tags: [pangenomics, theoretical, beginner]
- title: A pangenomics exercise
type: tutorial
url: https://merenlab.org/tutorials/vibrio-jasicida-pangenome/
authors: [meren]
summary: "A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course."
tags: [pangenomics, hands-on, beginner]
- title: An exercise on single-cell genomics
type: tutorial
url: /tutorials/single-cell-genomics-workshop/
authors: [FlorianTrigodet]
summary: "A hands-on tutorial to learn how to integrate single-cell genomics data. It covers functional and taxonomic assignment, pangenomic and phylogenomic analyses, and more."
tags: [pangenomics, phylogenomics, hands-on, beginner]
- title: Anvi'o phylogenomics workflow
type: tutorial
url: https://merenlab.org/2017/06/07/phylogenomics/
authors: [meren]
summary: "A comprehensive description of the anvi'o phylogenomics workflow."
tags: [phylogenomics, theoretical, beginner]
- title: An exercise on metabolic reconstruction in anvi'o
type: tutorial
url: /tutorials/fmt-mag-metabolism/
authors: [ivagljiva]
summary: "A hands-on exercise for the metabolism suite of programs in anvi’o. It starts with a section on how to estimate metabolism for a single bacterial isolate, and goes into larger, real-world dataset of metagenome-assembled genomes to demonstrate how to estimate metabolism compute enrichment scores for metabolic modules."
tags: [metabolism, metabolic-enrichment, genomics, metagenomics, hands-on, beginner]
- title: Anvi'o tools for microbial population genetics
type: tutorial
url: https://merenlab.org/2015/07/20/analyzing-variability/
authors: [ekiefl, tdelmont, meren]
summary: "A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output."
tags: [microbial-population-genetics, theoretical, intermediate]
- title: A primer on anvi'o with the Infant Gut Dataset
type: tutorial
url: https://merenlab.org/tutorials/infant-gut/
authors: [meren, ivagljiva, ekiefl, tdelmont]
summary: "A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset."
tags: [metagenomics, binning, pangenomics, phylogenomics, microbial-population-genetics, hands-on, beginner]
- title: A metagenomics workshop featuring anvi'o
type: tutorial
url: https://merenlab.org/tutorials/dfi-metagenomics-workshop/
authors: [ivagljiva, mschecht]
summary: "Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation."
tags: [metagenomics, metabolism, hands-on, beginner]
- title: Another anvi'o workshop on metagenomics
type: tutorial
url: /tutorials/microbiome-center-workshop/
authors: [ivagljiva, mschecht]
summary: "Materials and a tutorial from the 2023 iteration of our metagenomics workshop."
tags: [metagenomics, metabolism, hands-on, beginner]
- title: Scaling up your analysis with workflows
type: tutorial
url: /tutorials/scaling-up/
authors: [FlorianTrigodet]
summary: "Using publicly available genomes and metagenomes, and anvi'o build in snakemake workflow to contextualize a genome of interest."
tags: [metagenomics, pangenomics, hands-on, beginner]