16S-Pipeline: A comprehensive web-based platform for end-to-end 16S rRNA amplicon sequencing analysis.

Area of Science:

• Microbiology
• Bioinformatics
• Computational Biology

Background:

• 16S rRNA gene sequencing is crucial for microbial community analysis.
• Existing bioinformatics tools are fragmented, posing challenges for researchers.
• A unified, user-friendly platform is needed to streamline data analysis.

Purpose of the Study:

• To introduce 16S-Pipeline, an open-source, web-based platform for comprehensive 16S rRNA gene data analysis.
• To provide a complete workflow from raw sequence data to publication-ready results.
• To enable researchers without command-line expertise to perform complex microbiome analyses.

Main Methods:

• Automated detection of sequencing type, variable region, and platform.
• Quality filtering, primer trimming, and Amplicon Sequence Variant (ASV) inference using DADA2.
• Taxonomy assignment (SILVA v138.1), phylogenetic tree construction, and functional prediction (PICRUSt2).
• Downstream analyses including diversity metrics, differential abundance testing (multiple methods), and KEGG pathway mapping.
• Integration with NCBI SRA for data retrieval and deposition.

Main Results:

• 16S-Pipeline offers a complete workflow from raw FASTQ files to statistical analyses.
• The platform supports various sequencing types and platforms (Illumina, PacBio HiFi, Nanopore).
• It includes automated downstream analyses and visualization tools.
• Built-in NCBI SRA integration facilitates data management.
• The web interface simplifies complex analyses for non-experts.

Conclusions:

• 16S-Pipeline democratizes microbiome data analysis by providing an accessible, integrated platform.
• The tool reduces the technical barrier for researchers, accelerating microbiome research.
• It facilitates reproducible and publication-ready microbiome data analysis and deposition.