- Discover More / Long-Read Amplicon Analysis
Long-Read Amplicon Analysis
Comprehensive profiling for microbial communities
SeqCoast’s end-to-end amplicon analysis pipeline transforms raw sequencing data into key insights, revealing who’s in the community and how diverse it is. Our reproducible, publication-ready reports combine taxonomic profiling, diversity and phylogenetic analyses, and interactive visualizations in a single comprehensive deliverable.
Long-Read Amplicon
What is amplicon analysis?
Amplicon analysis enables the characterization of complex microbial communities directly from sequencing data. SeqCoast’s amplicon sequencing pipeline identifies microbial taxa, evaluates community diversity, and provides publication-ready visualizations and reports.
Amplicon analysis has applications across fields including:
- Soil health, crop productivity, and agricultural microbiology
- Clinical, translational, and infectious disease research
- Water quality, wastewater, and environmental monitoring
- Microbial communities associated with human health
- Comparative analysis of microbial communities across treatments, conditions, or timepoints
What's included?
Our report includes accessible, high-quality analysis results ready for publication.
Publication-ready analysis
- Fully reproducible and comprehensive report with interactive visualizations and data.
- Standalone versions of all figures and tables.
- Clear, organized file access instructions.
Documentation of methods and citations
- Method descriptions provided for publication process.
- Software versions maintained and managed in GitHub and Seqera Nextflow.
- Citations provided for publication reference.
Quality control
- Every order is reviewed by an expert bioinformatics scientist to ensure accurate, high-quality results.
- Interactive MultiQC report summarizes sequencing and processing quality metrics.
Analysis process
Our analyses are built with state-of-the-art computational tools and industry-standard quality control tools tailored to our workflow.
Taxonomic Profiling with Minimap2
- Classification of thousands of microbial species.
- Standardized taxonomic abundance tables.
- Interactive visualizations for exploration of microbial communities.
Alpha Diversity Analysis with Python
- Per-sample diversity analyses including richness, evenness, Simpson, Shannon, and Fisher’s alpha indices.
Quality control with FastCat and Samtools
- Quality control throughout, including general sequencing quality metrics.
Alpha Diversity Analysis
Alpha Diversity Analysis sample
Quality Control
Class-level abundance heatmap with sample clustering
Need something beyond the standard workflow?
We understand that some research requires specialized attention. Customized processing, reporting, and bioinformatics analyses are available for specialized research projects.
Pricing — the more you order, the lower the price!
Why order SeqCoast analysis?
Get interpretable results, not just a folder of output files. Transform raw sequencing data into actionable insights.
Save time with analysis infrastructure that's ready to scale from pilot studies to enterprise-scale projects.
Reduce cost and complexity by leveraging our established cloud computing environment and validated workflows.
Accelerate research with rapid turnaround times and high-throughput processing capabilities.
Skip building and maintaining a long-read amplicon pipeline of your own, at any batch size.
Trust your results with rigorous QC, proven pipelines, and expert scientific review.
Data delivery, security, and access
- Our analysis pipelines are managed by bioinformatics experts using modern, version-controlled workflow frameworks that enable standardized, documented, and reproducible analyses.
- We maintain security controls designed to protect customer data throughout the data lifecycle. All data are produced and analyzed on USA-based equipment and AWS cloud infrastructure. Learn more about our world-class informatics processes here.
We make it easy to access your data!
- Data delivery options include SFTP Download, AWS transfer, Box.com, and alternatives on request.
- Data are stored on AWS cloud infrastructure in the United States, providing scalable storage, high availability, and industry-recognized security controls.
Frequently Asked Questions
Can this identify fungi and viruses?
Our pipeline can identify and profile fungi within a sample when profiled by the ITS subunit. If you are interested in profiling fungi and bacteria together, we encourage you to connect with our team to determine whether two analyses (16S and ITS) are the best option.
Identification of viruses usually relies on amplification of sequences known to be found within specific viruses of interest, or whole-genome sequencing. If you are interested in identifying viral populations, we would be happy to meet with you to determine the best approach for your experiment.