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BacterialSeq – Nanopore Bacterial Genome Sequencing

BacterialSeq – Nanopore Bacterial Genome Sequencing
 
 

De novo bacterial genome sequencing and annotation with Oxford Nanopore long-read technology

Microsynth’s BacterialSeq service reconstructs complete bacterial genomes using Oxford Nanopore long-read sequencing and a dedicated bioinformatics pipeline. The workflow delivers high-quality de novo assemblies with annotation, variant analysis, and multiple species identification approaches — providing a comprehensive genetic profile of your bacterial isolate.

This service is available for DNA samples or bacterial pellets in tubes, and optional DNA isolation can be added.

 

What You Can Achieve

  • Obtain the complete bacterial genome sequence in a single experiment
  • Identify species and strain-level differences using three complementary methods (Kraken, ANI, BUSCO)
  • Detect mutations and structural variants relative to a reference genome
  • Verify plasmids present in your isolate (≥1 kb, copy number ≥3)
  • Evaluate genome completeness and assembly quality
  • Save time and resources compared to hybrid sequencing or multi-step workflows

Bioinformatics Analysis

With BacterialSeq, you receive all essential results for complete bacterial genome characterization — clearly structured and ready to use:

  • Assembled genome (.fasta) – high-quality de novo assembly from Nanopore reads
  • Annotated genome (.gbk) – genome features annotated via NCBI’s PGAP pipeline
  • Genome map (.pdf) – visual overview of contigs, gene density, and GC content
  • Species identification report – results from three complementary methods (Kraken, ANI, BUSCO)
  • Quality summary – coverage, completeness, and variant overview ensuring data reliability

Turnaround Time

  • Results within 1–3 working days after sample receipt
  • Results delivered Monday to Friday

Use our Microsynth drop boxes for free and convenient shipment.

Add-On Services

Enhance your BacterialSeq workflow with optional services:

  • DNA Isolation – Send bacterial pellets and let Microsynth perform DNA extraction.
  • Large Genome – For genomes between 7–12 Mb.
  • Polishing (Hybrid Assembly) – Further improve accuracy using Illumina short-read sequencing.
  • Variant Analysis – Identify and report mutations relative to a provided reference genome.
  • NAP Buffer Shipment – Safely ship bacterial cells at ambient temperature for isolation; can be ordered together with labels.

How to Order

Order labels for our BacterialSeq:
  • Enter our webshop
  • Click on BacterialSeq in the "Order Labels" area and follow the further instructions
  • Only choose non-prepaid labels for the BacterialSeq
 
Order BacterialSeq for sequencing:
  • Enter our webshop
  • Click on Tubes (DNA samples) or Tubes incl. Isolation (cell pellets) under "BacterialSeq" and follow the further instructions

See also Microsynth's user guide on the right side for more detailed information.