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.
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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.
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|
1.8 < OD260/280 < 2.0, 1.8 < OD260/280 < 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.