Our viral whole genome sequencing platform leverages the power of next-generation sequencing and long-read sequencing approaches (primarily Illumina HiSeq, Nanopore, and PacBio SMRT sequencing) to help you gain an insight into viral/phage structural genomics and comparative genomics. Based on the viral whole-genome sequencing platform, we provide both resequencing and de novo sequencing strategies to construct draft or complete viral/phage genomes.
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The automated and excellent vrial whole genome sequencing platform at CD Genomics enables us to sequence and assemble complete viral/phage genomes de novo or with the help of the reference genome. We perform PacBio SMRT (10/20 Kb library, 100-150X) and/or Illumina HiSeq PE150 (300-500 bp library, 100-200X) sequencing based on your sample type. PacBio SMRT sequencing can produce long reads, which is advantageous for genome assemblies, especially in GC-rich and repeat-dense regions. And illumina HiSeq sequencing is well-accepted due to its high throughput and accuracy. After sequencing, raw data are processed by quality control, trimming, and filtering. Accurate reads are then used for gap-closed genome assemblies or draft genome assemblies based on your needs.
Based on our viral whole-genome sequencing platform, we offer reliable viral whole-genome resequencing, de novo sequencing, and genome survey sequencing services. The resulting genome assemblies are confidential and ready for synteny analysis, variation analysis, and evolutionary analysis. Viral whole genome sequencing is also a tool for understanding the biochemical interactions between prokaryotic cells and phages, and has been widely applied to food industry and medical research. For example, multi-drug resistance is increasing sharply, and phage therapy is an efficient way to treating bacterial infections. Viral whole genome sequencing can help promote the development and spread of phage therapy in the United States and other countries.
Our bioinformatics analysis involves five parts: data quality control, genome 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 sequencing.
|Data QC||Removal of low-quality reads and adapter sequences|
|Genome assembly||De novo genome assembly, Reference-guided genome assembly|
|Genome assessment||Prediction of repetitive sequence, non-coding RNA, etc.|
|Functional annotations||KEGG, SwissProt, eggNOG, TrEMBL|
|Comparative genomic studies||Detection of variants (SNP, InDel), conserved genes, and unique genes, Viral evolutionary studies, correlation analysis, Gene expression correlation analysis|
1.8 < OD260/280 < 2.0, 1.8 < OD260/280 < 2.0, no degradation or contamination. DNA/cDNA amount ≥ 1 ug
Deliverables: raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, statistic data, and your designated bioinformatics report.