Whole genome sequencing is divided into de novo sequencing and whole genome resequencing. Sequencing a new instance of a species that already has a reference genome is known as resequencing. It is much easier to discover what makes the new bacterial genome different from the reference gene than to assemble a new reference genome. What the genome looks like and the location of the genes are both known. We use read mapping, instead of assembling a new genome sequence. We look for the most similar part of the reference genome for every sequence read from the new microbe and place it there. We can then find the differences between the reference genome and the mapped reads, which represent mutations in the new microbe genome.
Fig.1 Genome map of K. pneumonia 2N3. (Zhang C, et al. 2019)
Microbial whole genome resequencing can assist researchers in discovering single nucleotide polymorphism sites (SNPs), insertion, deletions and other mutation types. This sequencing method amplifies a single reference genome into the genetic characteristics of a biological population in the cheapest way. Paired-End sequencing is performed to detect the loci differences and structural variations between gene sequences and explain the reasons for the differences in traits at the whole genome level. It can also provide guidance and basis for screening the excellent traits of microbes, microbial resistance and other research.
Each whole genome resequencing project includes,
Our bioinformatics analysis covers a wide range including primary assembly and evaluation (K-mer analysis，GC-Depth analysis), and comparative genomic analysis (reference genome homology comparison, SNP/InDel, Phylogenetic analysis), etc.
In general, our turnaround time is 2-4 weeks depending on the size of your project.
Creative Biogene has excellent microbiology experts, well-established high-throughput sequencing platforms, and professional bioinformatics analysis to provide you with a one-stop service in whole genome resequencing. Our services include sample collection, quality control, library construction, sequencing and analysis.
If you are interested in our services, please contact us for more details.