Our microbial whole genome sequencing platform leverages the cutting-edge high-throughput sequencing technology to investigate the whole genome of novel or known microorganisms in an efficient and economical way. Our experienced scientists choose the most appropriate sequencing strategy and data analysis pipeline based on your sample and research purpose. With the microbial whole genome sequencing platform, we provide bacterial whole genome sequencing, fungal whole genome sequencing, yeast whole genome sequencing, and viral whole genome sequencing.
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The microbial whole genome sequencing platform at CD Genomics is an automated and intelligent platform utilizing Illumina HiSeq sequencing, PacBio SMRT sequencing, and/or Nanopore sequencing. It resolves whole genome assemblies, especially for repeat-dense and GC-rich genomes, as well as plasmids. This platform can be used to sequence the complete genome of bacteria, fungi, viral/phage, archaea, algae, and protozoa by microbial de novo sequencing or resequencing. Based on the resulting genomic information, it is viable to predict the functional elements of the genome, annotate gene function, and conduct comparative genome studies, identify single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels), and discover other genetic alterations among microbial strains.
Microbial whole genome sequencing further characterizes microbial methylomes. These medications may serve as a defense mechanism in microbes or regulate certain biological processes in bacteria, such as DNA replication, gene expression, DNA repair, and cell cycle. With the capability of characterizing closed microbial reference genomes and methylomes with confidence and ease, this platform has significant advantages in clarifying the role of structural variants in the evolution of virulence, and addressing issues of drug resistance and transmission paths, as well as disease outbreaks.
For different research purposes, CD Genomics has different sequencing strategies. For draft genome and microbial resequencing, we recommend Illumina HiSeq PE150 sequencing. For complete genomes, we recommend PacBio SMRT sequencing. And we ensure the 50-fold (at least) coverage of PacBio SMRT sequencing data and 100-fold (at least) coverage of Illumina Hiseq PE150 sequencing data.
Our bioinformatics analysis involves five parts: data quality control, genome assembly and quality control, prediction of functional elements, gene function annotation, and comparative genome analysis. For more details, please refer to the following table.
Table 1. Our bioinformatics analysis for microbial whole genome sequencing.
|Data QC||Removal of poor-quality reads and adapter sequences|
|genome assembly||Reference-standard genome assembly.
Genome assessment including genome size, GC content, non-identity sequence, and plasmid sequence.
|Functional elements||Prediction of functional elements including coding sequence, non-coding RNA, repeat sequence, prophage, CRISPR, and genome island.|
|Gene function annotation||GO, KEGG, NR, COG, Swiss-Prot, Pfam, TCDB, CAZy, PHI, P450, etc.|
|Comparative genome analysis||SNP/Indel analysis, Ka/Ks analysis, phylogenetic analysis, synteny analysis.|
1.8 < OD260/280 < 2.0, OD260/230 ≥ 1.8, 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.