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Short-Read Amplicon Analysis
SeqCoast’s short-read amplicon analysis pipeline transforms raw sequencing data into key insights: who’s in the community, how diverse is it, and which antibiotic resistance genes are present.
Amplicon Analysis
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, conducts functional annotation, and provides publication-ready visualizations and reports. Our reproducible reports combine taxonomic profiling, diversity and phylogenetic analyses, and interactive visualizations in a single comprehensive deliverable.
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.
- Classification of thousands of microbial species.
- Standardized taxonomic abundance tables.
- Interactive visualizations for exploration of microbial communities.
Optional group-wise comparisons across metadata-defined sample groups including:
- Alpha diversity calculations and visualizations.
- Beta diversity community analyses using multiple distance metrics.
- Prediction of functional potential of communities based on marker gene sequences.
- Profiling and visualization of species relatedness within samples.
- Methods, software versions, citations, and thorough FAQs included in every order.
- Optional host sequence depletion of host-associated samples.
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 short-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
Which diversity metrics are calculated?
Our pipeline reports on a range of both alpha (within-sample) and beta (across-sample) diversity metrics, including evenness, richness, Faith’s pd, Bray-Curtis, Jaccard, weighted/unweighted Unifrac, and more
Is analysis performed on ASVs or OTUs?
This pipeline conducts analysis on ASVs (amplicon sequence variants) rather than OTUs (operational taxonomic units). Multiple sequences can make up one OTU, whereas an ASV is defined as a single amplicon sequence. In recent years the field has shifted away from using OTUs, which offer lower resolution, in favor of ASVs, which are more specific.
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.