Florian Trigodet of anvi'o
Bio
Microbiologist using advanced computational strategies to make sense of the microbial ecology of complex habitats.
Affiliations
currentSenior Scientist, Alfred Wegener Institute for Polar and Marine ResearchcurrentSenior Scientist, Helmholtz Institute for Functional Marine BiodiversitycurrentAssociate Junior Fellow, Hanse-Wissenschaftskolleg, Institute for Advanced StudypastPost-doctoral Scientist, Helmholtz Institute for Functional Marine BiodiversitypastPost-doctoral Scientist, The Department of Medicine at the University of Chicago
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Intellectual contributions
Some contributions are more than code. Inevitably, this manually curated list will be incomplete for almost everyone, but nevertheless, we try to keep track of key contributions made by memebers of the anvi'o commmunity to the platform and its users. Edit these files to help.
- Led the design and development of core anvi'o programs and workflows.
- Made significant contributions to anvi'o educational materials, maintained active engagement with the anvi'o user and developer community.
- Spearheaded the development of anvi'o framework to study genomic inversions.
- Made significant contributions to improving the performance of various anvi'o programs and workflows, including anvi-profile and EcoPhylo, by reducing the memory requirements, storage fingerprint, and runtime.
- Made significant contributions to the overall health and maintenance of the codebase through performance refactoring, feature implementation, and issue diagnoses.
- Organized and taught free-to-attend anvi'o workshops.
Resource contributions
Tutorials and exercises
Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.
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.
Using publicly available genomes and metagenomes, and anvi'o built-in snakemake workflows to contextualize a genome of interest.
A multi-purpose tutorial based on human oral microbiome data
Articles, workflows, opinions
Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.
An application of metagenomic long-read sequencing, assembly, correction, and the use of anvi'o pangenomics workflow to benchmark outcomes.