Charlie Pauvert
Chercheur Postdoctoral at Uniklinik RWTH Aachen
Aachen, North Rhine-Westphalia, Germany
Summary
👤
Senior🎓
Top SchoolCharlie Pauvert is a postdoctoral researcher and interaction-focused bioinformatician based in Aachen with 11 years of experience applying metagenomics, statistical modeling, and workflow engineering to microbial ecology problems. Trained with a PhD in evolutionary, functional and community ecology, he has benchmarked metabarcoding pipelines, inferred microbial networks, and validated interaction hypotheses experimentally and by text-mining. As a prolific contributor to the Snakemake wrappers repository, he has implemented and improved many DADA2 workflow components, bridging reproducible workflows and practical bioinformatics. A motivating team player and open-source enthusiast, he pairs rigorous computational methods with hands-on experimentation, and off the bench you’ll find him boxing, running, or testing new recipes.
11 years of coding experience
2 years of employment as a software developer
Master's degree, Bioinformatics, Master's degree, Bioinformatics at Université de RouenDoctorat, Evolutionary, Functional and Community Ecology, Doctorat, Evolutionary, Functional and Community Ecology at Université de BordeauxBachelor's degree, Life Science, Bachelor's degree, Life Science at Université Pierre et Marie Curie (Paris VI)
Github Skills (10)
bioinformatics10
work-flow10
snakemake10
python10
r10
pytest9
testing9
yaml8
dockers3
docker3
Programming languages (10)
Github contributions (5)
snakemake/snakemake-wrappers
Oct 2020 - Nov 2020
This is the development home of the Snakemake wrapper repository, see
Role in this project:
Data Scientist / Bioinformatics Engineer
Data Scientist / Bioinformatics EngineerContributions:61 reviews, 20 commits, 26 PRs in 1 month
Contributions summary:Charlie primarily contributes to the development of Snakemake wrappers, focusing on bioinformatics tools. They implemented wrappers for various DADA2 functions, including quality profile analysis, error rate learning, filtering/trimming, dereplication, merging paired reads, sequence table creation, taxonomy assignment, chimera removal, species annotation, and sequence collapsing. Their contributions involve creating new wrappers, modifying existing ones, and improving documentation, tests, and integration with the Snakemake workflow system. The user demonstrates strong understanding of DADA2, bioinformatics data analysis techniques, and workflow design.
snakemake
cpauvert/cpauvert.github.io
Jul 2016 - Oct 2020
Contributions:7 pushes, 2 branches in 4 years 3 months
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