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Bacterial Genome Sequencing, De Novo Assembly and Annotation - Illumina Test

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Bacterial Genome Sequencing, De Novo Assembly and Annotation - Illumina Test

Short Name: Bacterial Genome Sequencing

Also known as: Bacterial Whole Genome Sequencing, WGS for Bacteria, De Novo Bacterial Genome Assembly

Bacterial Genome Sequencing, De Novo Assembly and Annotation - Illumina Test test available at DNA Labs India for ₹30,000. Uses Illumina Sequencing, De Novo Assembly, Genome Annotation on Extracted DNA samples. Results in Reports are typically available within 8 weeks from the date of sample receipt.. Free home collection in 300+ cities across India.

Molecular🏠 Home Collection

✍️ Written By

🩺 Medically Reviewed By

Dr SULOCHANA HEMCHANDRA HOLLA

Dr SULOCHANA HEMCHANDRA HOLLA

Consultant Medical Geneticist · Reg: 8532

Last reviewed: September 7, 2026

Overview

The purpose of bacterial genome sequencing, de novo assembly, and annotation is to provide a comprehensive genetic blueprint of a bacterial isolate. This information is used to identify the species and strain, detect antimicrobial resistance determinants, assess virulence potential, and perform epidemiological typing. It aids in outbreak investigations, tracking transmission routes, and understanding the evolution of pathogenic bacteria. Ultimately, this test supports personalized treatment decisions, infection control measures, and the development of novel therapeutic targets.

Test Code
6337
CPT Code
N/A
ICD Code
N/A
Price
₹30,000
Sample Type
Extracted DNA
Result Time
Reports are typically available within 8 weeks from the date of sample receipt.
Fasting Required
No
Method
Illumina Sequencing, De Novo Assembly, Genome Annotation
Step 1

Sample Collection

Ensure the bacterial isolate is pure and grown on appropriate media. For clinical specimens, follow standard collection protocols. Inform the laboratory about any prior antibiotic treatment.

Method: DNA extraction from bacterial culture or clinical specimen

Step 2

Laboratory Analysis

Sample collection should be performed under sterile conditions to avoid contamination. For extracted DNA, use certified nuclease-free tubes and avoid freeze-thaw cycles.

Step 3

Report Delivery

Store the sample at -20°C or -80°C if not processed immediately. Ship on dry ice to the laboratory.

Timeline: Reports are typically available within 8 weeks from the date of sample receipt.

Patient Instructions

1
Before the Test:No special preparation is required. However, ensure that the bacterial isolate is provided in pure culture for optimal results.
2
During the Test:The sequencing process involves DNA fragmentation, adapter ligation, and cluster generation followed by sequencing on the Illumina platform. Bioinformatics analysis includes quality trimming, de novo assembly, and annotation.
3
After the Test:You will receive a comprehensive report detailing the genome assembly, annotation, and identified features. Discuss the results with your healthcare provider for clinical interpretation.

About This Test

Who Should Get This Test

The purpose of bacterial genome sequencing, de novo assembly, and annotation is to provide a comprehensive genetic blueprint of a bacterial isolate. This information is used to identify the species and strain, detect antimicrobial resistance determinants, assess virulence potential, and perform epidemiological typing. It aids in outbreak investigations, tracking transmission routes, and understanding the evolution of pathogenic bacteria. Ultimately, this test supports personalized treatment decisions, infection control measures, and the development of novel therapeutic targets.

How to Prepare

  • For bacterial culture: provide a pure culture on agar slant or in transport medium.
  • For clinical specimens: collect in sterile containers as per standard guidelines.
  • For extracted DNA: ensure concentration ≥ 20 ng/µL and OD260/280 between 1.8-2.0.

Doctor's Notes

Reviewed by — MBBS, MD (Medical Genetics) · Reg. No. 8532

"Bacterial genome sequencing provides critical insights into antimicrobial resistance and virulence, guiding targeted therapy and infection control."

Last medically reviewed: September 7, 2026

Test Parameters & Specifications

Sample TypeExtracted DNA
Sample Volume1-2 µg (concentration ≥ 20 ng/µL)
ContainerSterile microcentrifuge tube
Collection MethodDNA extraction from bacterial culture or clinical specimen

Sample Stability

Extracted DNA: stable for 1 week at 4°C, 6 months at -20°C, and 1 year at -80°C.
Bacterial culture: stable for 48 hours at 2-8°C, longer at -70°C in glycerol stock.
Sample Rejection Criteria:
  • Insufficient DNA quantity or quality
  • Hemolyzed or contaminated samples
  • Improper labeling or documentation
  • Sample not stored or transported under recommended conditions

Understanding Your Results

The results of bacterial genome sequencing provide a comprehensive genetic profile of the organism. The interpretation should be performed by a qualified geneticist or microbiologist in conjunction with clinical findings.
Species identification: Based on average nucleotide identity (ANI) and phylogenetic analysis.
Antimicrobial resistance: Presence of known resistance genes (e.g., blaNDM, mecA) indicates potential resistance; correlation with phenotypic susceptibility is recommended.
Virulence factors: Detection of genes encoding toxins, adhesins, or secretion systems suggests pathogenic potential.
Typing: Multi-locus sequence typing (MLST) or core genome MLST (cgMLST) for epidemiological relatedness.
Plasmids: Presence of plasmid replicons may indicate mobile genetic elements carrying resistance or virulence genes.
⚠️ When to Consult a Doctor:

Consult your physician if you have persistent or recurrent bacterial infections, or if you require guidance on antimicrobial therapy based on genomic results.

Limitations

  • ⚠De novo assembly may not resolve highly repetitive regions or plasmids completely
  • ⚠Annotation accuracy depends on reference databases and algorithms
  • ⚠Detection of resistance genes does not always correlate with phenotypic resistance
  • ⚠Requires high-quality extracted DNA; degraded samples may yield incomplete results

Risks & Considerations

  • ●No significant physical risks are associated with this test as it is performed on extracted DNA or bacterial culture.
  • ●Potential psychological impact from unexpected findings such as resistance or virulence traits.

Interfering Factors

  • ●Contamination with host or environmental DNA
  • ●Low DNA quantity or quality
  • ●Incomplete sequencing coverage
  • ●Presence of repetitive regions
  • ●Chimeric reads during assembly

Compare With Similar Tests

TestBacterial Genome Sequencing, De Novo Assembly and Annotation - Illumina
ComparisonBacterial Genome Sequencing, De Novo Assembly and Annotation - Illumina

Frequently Asked Questions

What is bacterial genome sequencing?
Bacterial genome sequencing determines the complete DNA sequence of a bacterial genome using high-throughput technologies like Illumina.
What is de novo assembly?
De novo assembly reconstructs the genome from short DNA reads without a reference, producing contiguous sequences (contigs).
What is annotation?
Annotation identifies genes, regulatory elements, and functional features in the assembled genome using computational tools.
Why is this test important?
It helps understand bacterial virulence, drug resistance, and evolution, aiding in treatment and infection control.
What is the cost of this test?
The cost is INR 30000 per sample, inclusive of home collection and analysis.
What sample is required?
Extracted DNA from a bacterial culture or clinical specimen is required.
How long does it take to get results?
Reports are available within 8 weeks.
Is fasting required?
No, fasting is not required for this test.
Can I get a home sample collection?
Yes, free home sample collection is available for online bookings across India.
What does the report include?
The report includes genome assembly statistics, annotation, resistance genes, virulence factors, and phylogenetic analysis.
How accurate is Illumina sequencing?
Illumina sequencing has high accuracy (greater than 99.9%) for base calling.
Are there any risks?
No significant physical risks; the test is performed on extracted DNA or culture.
Worried about the process? Our certified phlebotomists collect thousands of samples every month across India. The process takes under 5 minutes and is virtually painless. Questions? Message us on WhatsApp — we're here 7 days a week.

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For Hospitals & Clinics

Reference Laboratory Services

We serve as a reference laboratory for hospitals and clinics across India. Send samples from your facility with same-day pickup, priority processing, and results delivered through our online portal. Competitive institutional pricing available.

LIMS Integration

Your Data Privacy

Your medical data is protected under Indian law.

✓ Stored in India: All patient records are stored on servers located in India. No data is transferred outside the country.

✓ DPDP Act Compliant: Under the Digital Personal Data Protection Act 2023, you can request deletion of your records at any time by contacting support.

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