At SNPcode, long-read sequencing technological strengths are coupled with stringent quality control and specialised bioinformatics workflows, ensuring robust, high-confidence microbial datasets.

SNPcode Workflow for Full-Length 16S / ITS Sequencing

1. Sample Preparation

   • DNA extraction optimised for different sample types: clinical (stool, saliva, tissue), soil, water, food, and industrial matrices.

   • Assessment of DNA quality and concentration (Qubit, Nanodrop, agarose gel).

2. Amplicon Generation & Library Preparation

   • PCR amplification of the near-full-length 16S rRNA gene (~1.5 kb) / ITS using universal primers.

   • Verification of amplicon integrity and yield.

   • ONT-specific library preparation, with optional barcoding for multiplexing.

3. Oxford Nanopore Sequencing

   • Long-read sequencing on ONT platforms (MinION/PromethION).

   • Monitoring of read length distribution and data yield in real time.

4. Bioinformatics Analysis

   • Basecalling and demultiplexing of raw reads.

   • Quality filtering and adapter trimming.

   • Taxonomic classification using curated 16S databases (SILVA, RDP, GTDB).

   • Diversity analysis (alpha/beta metrics), community composition profiling, and phylogenetic tree construction.

5. Reporting

   • Comprehensive reports with taxonomic summaries, relative abundance plots, and diversity indices.

   • Publication-ready figures and data formats tailored to specific research or regulatory requirements.

Applications Across Industries

• Healthcare & Clinical Microbiology – Human microbiome characterisation, pathogen detection, antimicrobial resistance surveillance.

• Agriculture & Soil Microbiology – Soil biodiversity studies, rhizosphere microbiota profiling, crop-associated microbial interactions.

• Food & Beverage Industry – Detection and monitoring of microbial contaminants, spoilage organisms, and probiotics.

• Environmental Microbiology – Profiling of microbial diversity in aquatic and terrestrial ecosystems, wastewater monitoring.

• Industrial Biotechnology – Monitoring microbial consortia in fermentation and bioprocesses.

Why Partner with SNPcode Pvt Ltd?

✅ State-of-the-art Oxford Nanopore platforms for full-length 16S rRNA sequencing.

✅ Rigorous QC and bioinformatics pipelines for high-confidence taxonomic assignments.

✅ Flexible project design – from pilot studies to large-scale metagenomic surveys.

✅ Fast, cost-effective services with customizable reporting options.

At SNPcode, we provide not just raw sequencing data but actionable microbial insights to advance research and industrial applications.

Conclusion

Full-length 16S / ITS sequencing via Oxford Nanopore Technologies bridges the gap between traditional region-specific sequencing and whole-genome metagenomics, offering high-resolution microbial profiling with reduced bias.

By integrating this technology with expert bioinformatics, SNPcode enables researchers and industries to gain deeper insights into microbial communities, supporting innovation across healthcare, agriculture, food safety, and environmental sciences.

📩 Contact us today to discuss your research needs and explore how full-length 16S / ITS sequencing can enhance your microbiome studies.