Bacterial Whole Genome Resequencing

Overview

Our microbial whole genome resequencing platform utilizes the cutting-edge high-throughput sequencing technology (including Illumina and PacBio SMRT platforms) to detect bacterial SNPs/InDels/SVs/CNVs in an efficient and economical way. We offer reliable sequencing approaches and confidential bioinformatics analysis to help you gain an insight into functional elements, functional genes, and phylogeny.

Our Advantages:

Extensive experience.
More than 70% of our team is PhD and Masters-level scientists.
Targeted region sequencing, enabling a rapid and efficient workflow.
Both Illumina PE250/300 and PacBio systems are available.

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We are dedicated to providing outstanding customer service and being reachable at all times.

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Introduction to Our Bacterial Whole Genome Resequencing

The automated and excellent bacterial whole genome resequencing platform at CD Genomics enables high-effective and affordable microbial whole genome resequencing. We perform PacBio SMRT (100-150X) or Illumina HiSeq PE150 (300-500 bp insert DNA library, 50-100X) sequencing with your samples. PacBio SMRT sequencing generates long reads and Illumina sequencing is characterized by high throughput and high accuracy rate. After raw data QC and filtering, qualified reads are aligned to the reference genome for detection of variants, including single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), structure variations (SVs), and copy number variations (CNVs). These molecular markers can further be functionally annotated and used for studies of evolution, population characterization, and selective pressure.

Unlike PCR-based or capillary sequencing approaches, next-generation sequencing (NGS)-based microbial whole genome resequencing allows researchers to sequence hundreds of organisms with the power of multiplexing. At the same time, it simplifies the workflow and saves time. NGS can identify low-frequency variants and genome rearrangements in an efficient and economical way.

Our bacterial whole genome resequencing platform enables researchers to conduct research on disease outbreaks and treatments, as well as drug development and microbial control in many fields. If your microbial samples have no reference genomes, we also have bacterial whole genome de novo sequencing platform that generates accurate reference genomes, which are useful for microbial identification and comparative genomic studies.

Bacterial Whole Genome Resequencing Workflow

Bioinformatics Analysis

Our bioinformatics analysis involves four parts: data quality control, sequence alignment, polymorphism detection, and variant annotations. For more details, please refer to the following table.

Table 1. Our bioinformatics analysis for microbial whole genome sequencing.

Procedures	Problem to be solved	Examples of tools
Data QC	Removal of poor-quality reads and adapter sequences	FastqQC, NGS-QC
Sequence alignment	Align qualified reads against the reference genome	BWA, Samtools
Polymorphism detection	Detect SNPs/InDels/SVs/CNVs and locate them to the genome	Samtools, GATK, CNVanotor, BreakDancer
Variant annotation	Variant expression profiling and variant function annotation

Sample Requirement

1.8 < OD_260/280 < 2.0, 1.8 < OD_260/280 < 2.0, no degradation or contamination. Illumina platform: prokaryotic/eukaryotic DNA/cDNA amount ≥ 2 μg, viral DNA/cDNA amount ≥ 1 ug PacBio platform: bacterial DNA amount ≥ 5 μg, fungal DNA amount ≥ 10 μg

Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, statistic data, and your designated bioinformatics report.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.