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Prokaryote Variant Calling
Profile genomic variants
SeqCoast’s prokaryote variant calling pipeline identifies genetic variation within a sample and reports findings within a single comprehensive deliverable. Our reproducible, publication-ready reports combine calling of SNPs, indels, structural changes, and CNVs for a range of variant insights.
Prokaryote Variant calling
What is variant calling analysis?
Prokaryote variant calling analysis enables the characterization of genomic variation within samples directly from sequencing data. SeqCoast’s prokaryote variant calling pipeline identifies and annotates single-nucleotide variants (SNPs), insertions and deletions (indels), structural variants, and copy number variants (CNVs), providing clear, publication-ready results and visual summaries.
Prokaryote variant calling analysis has applications across fields including:
- Translational, and infectious disease research
- Antimicrobial resistance research and pathogen surveillance
- Bacterial strain comparison
- Evolutionary, phylogenetic, and population genomics studies
- Comparative analysis of bacterial isolates across treatments, conditions, locations, 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.
QC and Preprocessing with Trimmomatic/Porechop
- Thorough quality preprocessing and quality control results.
Mutation analysis – SNPs, indels, and structural changes with Bowtie2 and Breseq
- Characterization of SNPs, indels, and structural changes, with detailed information on confidence of mutation calling
Mutation analysis – CNVs with CNOGPro
- Identification of copy number variations, relative to reference genome
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 prokaryote variant calling 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
Does this analysis require long or short reads?
This analysis can be performed on either long or short reads. If you are unsure which option is the best choice for you, get in touch with us to speak to our team of microbiologist experts.
Does this pipeline work for bacterial populations as well as clones?
Yes, the variant calling pipeline supports both clonal and mixed bacterial populations.
What additional information is required to perform this analysis?
To perform variant calling analysis, we require that you specify a reference genome to which you would like us to align your samples. Generally these can be found via RefSeq or GenBank.
No reference genome available for your samples? Consider bundling with our assembly and annotation pipeline to generate an annotated reference genome.