Our bacterial whole genome de novo sequencing platform leverages the power of high-throughput sequencing technology to generate accurate draft or complete genomes for microbial identification and comparative genomic studies. We provide 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 de novo sequencing platform at CD Genomics enables us to sequence bacterial genomes de novo. We perform PacBio SMRT sequencing (100-150X), Nanopore sequencing, and/or Illumina HiSeq PE150 (100-200X) sequencing to assembly complete bacterial genomes. PacBio SMRT sequencing generates long reads, which is important for genome assemblies especially in GC-rich and repeat-dense regions. And illumina HiSeq sequencing is characterized by high throughput and accuracy. After raw data QC, correction, and filtering, qualified reads are used to construct confidential draft or complete genomes based on your demands.
Genomic sequences are fundamental to study a species at molecular level. Bacterial whole-genome de novo sequencing is the best way to obtain the whole-genome sequence map of a species without reference genome. It allows bacterial identification, gene function analysis, variation studies, phylogenetic studies, and associated disease studies. It has been widely applied to multiple fields, such as bacterial evolution, epidemiological studies, vaccine and drug development, and bacterial control. If the reference genome is available, our bacterial whole genome resequencing platform can perform efficient and accurate genome assembly.
Our bioinformatics analysis involves five parts: data quality control, de novo assembly, genome assessment, functional annotations, and comparative genomic studies. For more details, please refer to the following table.
Table 1. Our bioinformatics analysis for microbial whole genome de novo sequencing.
| Analysis content | Details |
|---|---|
| Data QC | Removal of low-quality reads and adapter sequences |
| De novo assembly | Utilize software such as SOAPdenovo and SOAPdenovo2 to assemble reference-quality complete bacterial/fungal genomes. |
| Genome assessment | Detection of repetitive sequence, non-coding RNA, CRISPR, prophage, and genomic island. |
| Functional annotations | KEGG, SwissProt, GO, Nr, COG (for general functional annotations) |
| PHI (database of pathogen-host interaction) | |
| VFDB (database of virulence factors of bacterial pathogens) | |
| ARDB (database of antibiotic resistance) | |
| CAZy (database of Carbohydrate-Active enZYmes) | |
| And other databases... | |
| Comparative genomic studies | Detection of variants, conserved genes, and unique genes Construction of phylogenetic trees Gene family studies |
1.8 < OD260/280 < 2.0, 1.8 < OD260/280 < 2.0, Qubit/OD > 0.5, no degradation or contamination. Illumina platform: DNA/cDNA amount ≥ 2 μg, concentration ≥ 20 ng/μL PacBio platform: (Bacteria) DNA amount ≥ 5 μg, concentration ≥ 80 ng/μL、(Fungi) DNA amount ≥ 10 μg, concentration ≥ 80 ng/μL
Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, statistic data, and your designated bioinformatics report.
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