A5034654544- Fungal Infections and Studies
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Gene expression and cancer classification
- Antifungal resistance and susceptibility
- Gut microbiota and health
- Probiotics and Fermented Foods
University of Lausanne
2019-2024
Summary: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene bacteria archaea or ITS fungi. zAMP is complemented by two modules, one to process databases optimize taxonomy assignment, second benchmark primers, classifier performances. Coupled with zAMPExplorer, interactive R Shiny application that provides intuitive interface quality control,...
Abstract Summary The intrinsic complexity of the microbiota combined with technical variability render shotgun metagenomics challenging to analyze for routine clinical or research applications. In silico data generation offers a controlled environment allowing example benchmark bioinformatics tools, optimize study design, statistical power, validate targeted Here we propose assembly_finder and Metagenomic Sequence Simulator (MeSS), two easy-to-use Bioconda packages, as part benchmarking...