TaxoFlow: The Tutorial. An Educational Nextflow Pipeline for Metagenomics Taxonomic Profiling

Analysis reproducibility has become one of the main challenges for scientific reporting as it is critical to ensure transparent and comparable results. Metagenomics studies are not exempted from these concerning aspects, and hence bioinformatics pipelines to handle this type of data have evolved rapidly as an attempt to equip the research community with reliable methodologies and procedures. Nonetheless, as these workflows grow in robustness and complexity, inexperienced users find it difficult to understand or customize the pipelines. To address this limitation, we developed an open, interactive and web-based tutorial (TaxoFlow) that guides scholars through the detailed development of a validated and reproducible Nextflow metagenomics profiling pipeline. This workflow integrates software to remove host sequences (Bowtie2), a taxonomic classification (Kraken2), a tool for species abundance re-estimation (Bracken) and different data visualization strategies. As important features, the tutorial emphasizes simplicity, modularity, and containerization, which empowers users with both conceptual understanding and practical implementation skills. Noteworthy, this tutorial provides all the required files, databases, dependencies, software and environment for the user to run without the need of local installation or computational adaptations elsewhere. Finally, by offering a fully reproducible pipeline with a step-by-step developing tutorial, this work aims to lower technical barriers in microbiome bioinformatics and promote best practices in metagenomics data analysis. TaxoFlow is freely available at https://taxoflow.work/.