Microbial WGS | Nanopore Long-Read & Hybrid Sequencing

Overview

Quintara Microbial WGS provides whole-genome sequencing options for cultured bacterial and yeast samples, with Long-Read and Hybrid workflows designed to address different genome assembly and accuracy requirements. Long-Read Microbial WGS uses 30–50× Nanopore coverage to generate long reads that can span repetitive regions, resolve structural variations, and characterize other complex genomic features, making it well suited for de novo genome assembly. Hybrid Microbial WGS combines 30–50× Nanopore long-read coverage with 30–50× short-read coverage to provide high assembly continuity and improved consensus accuracy. Together, these workflows offer flexible solutions for reconstructing microbial genome structure and generating high-accuracy, polished genome assemblies.

Long-Read Advantage

Resolve repetitive and complex genomic regions
High-Quality Sequencing

Generate reliable whole-genome sequencing data
Accurate Consensus

Improve accuracy with complementary data
Flexible WGS Options

Choose the workflow that fits your research needs

What Is Nanopore Long-Read & Hybrid WGS Used For?

Create

Build a genome from scratch

Resolve

Reveal complex genome features and variation

Produce

Generate a highly accurate consensus genome

Create a de novo assembly without relying on a reference

Work with a complex or heterozygous yeast isolate

Resolve repeats and larger structural changes

Explore native-DNA methylation

Produce a highly polished consensus genome

Call SNVs and short indels against a known reference

Routine complete-genome work at the lowest listed price

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Workflow

An integrated workflow from DNA QC and library preparation to sequencing, genome assembly, polishing, and analysis, with Long-Read and Hybrid options tailored to different project needs.

Sample Submission

Cultured bacterial or yeast isolates
DNA QC & Library Prep

DNA QC and workflow-specific library preparation
Sequencing

30–50× Nanopore or Hybrid sequencing
Genome Assembly & Analysis

De novo assembly, polishing, and genome analysis
Data Delivery

Sequencing data, assemblies, and analysis results

Services

Service	Technology & Coverage	Sample Type	Price	Turnaround Time
Long-Read Microbial WGS	30–50x Nanopore long-read	Bacterial	Starting from $90	1-2 Business Days
		Yeast	$150
Hybrid Microbial WGS	30–50x Nanopore long-read + 30–50x NGS short-read	Bacterial	Starting from $165	5-10 Business Days
		Yeast	$255

* Your project clock starts once we receive your samples.

* DNA Extraction — $15 per sample. Available for both service options.

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Choose the Services According to Your Needs

	Long-Read Microbial WGS	Hybrid Microbial WGS
Technology	Nanopore long-read	Nanopore long-read + NGS short-read
Coverage	30–50× Nanopore	30–50× Nanopore + 30–50× NGS
Analysis Approach	De novo genome assembly	De novo hybrid assembly + polishing
Best For	Designed for de novo assembly and high-contiguity reconstruction of bacterial and yeast genomes, especially when resolving repeats, complex regions, and large structural variations is a priority.	De novo assembly when both high genome continuity and strong consensus accuracy are required, especially for reference-quality isolate genomes and publication-oriented projects.
Key Advantages	Long reads capture genome architecture without a close reference, with native-DNA methylation analysis available.	Combines Nanopore long reads for genome-wide structural resolution with short reads for improved base-level consensus accuracy.
Key Consideration	Consensus accuracy may be lower than hybrid-polished results, especially for small indels and challenging regions.	Higher cost and a more involved workflow than Long-Read WGS, while still representing a consensus genome rather than low-frequency variants.
Deliverables	• Sequencing & Assembly QC Report (HTML) • NanoPlot Sequencing QC • Bandage Assembly Visualization • CheckM Completeness & Contamination Assessment • Species Identification • De Novo Assembled & Annotated Consensus Genome • Raw Nanopore FASTQ Data • Methylation Analysis Report (optional)	• Sequencing, Assembly & Polishing QC Report (HTML) • NanoPlot Sequencing QC • Bandage Assembly Visualization • CheckM Completeness & Contamination Assessment • Species Identification • Polished, De Novo Assembled & Annotated Consensus Genome • Raw Nanopore FASTQ Data • Paired-End Short-Read FASTQ Data • Methylation Analysis Report (optional)

FAQ

Does higher sequencing coverage always mean better genome assembly?: Not necessarily. Coverage indicates how many times the genome is represented in the sequencing data, but it does not determine read length or assembly continuity. For de novo assembly, long reads can span repetitive and complex regions that very high-coverage short reads may still fail to connect.

What type of samples are suitable for Long-Read and Hybrid Microbial WGS?: Both workflows are designed for pure bacterial or yeast isolates and require high-quality genomic DNA. Mixed or contaminated samples may affect genome assembly and downstream analysis.

Does genome size affect the WGS service?: Yes. Organism type and expected genome size help determine sequencing requirements, data yield, and project pricing.

What does 30-50x coverage mean?: It means the total sequenced bases are roughly 30-50 times the expected genome size on average. Individual regions may receive more or less coverage.

Do I need a reference genome?: No. Both Long-Read and Hybrid WGS can generate a de novo assembly without relying on a close reference genome. A suitable reference may be used for additional reference-based analyses when needed.

How do I choose if I am unsure which service I need?: Choose Long-Read when the main goal is de novo assembly and genome structure, Hybrid when both assembly continuity and base-level confidence are important.

Can additional analyses, such as variant calling or methylation analysis, be requested?: Yes. Additional analyses, including reference-based mapping, variant calling, and methylation analysis, may be available depending on project requirements and service availability. Methylation analysis requires native DNA.

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