AmpWrap: a one-line fully automated amplicon metabarcoding 16S and 18S rRNA gene analysis.

Motivation: The revolution of next-generation sequencing has driven the establishment of metabarcoding as an efficient and cost-effective method for exploring community composition. Amplicon sequencing of taxonomic marker genes, such as the 16S rRNA gene in prokaryotes, provides an efficient method for high-throughput taxonomic profiling. The advent of long read technologies made it feasible to sequence the whole 16S rRNA gene rather than only a few regions, with the potential to achieve species-level resolution. Despite the affordability and scalability of such experiments, a major bottleneck remains the lack of integrated and user-friendly analytical workflows. Current pipelines often require the use of multiple tools with complex dependencies, and parameter optimization is frequently performed manually, limiting reproducibility and overall efficiency. Results: To address these limitations, we developed, AmpWrap, an automated, one line workflow designed to analyse both Illumina and Nanopore amplicons, requiring minimal efforts by the user and automatically optimizing the trimming parameter to retain the maximum number of reads and information while reducing noise. Availability and implementation: AmpWrap is available at: https://github.com/LDoni/AmpWrap.