WGS is essential in a wide range of scientific fields, both fundamental and applied. It can identify genetic variations across the genome, which is why it is commonly used in agriculture and evolutionary biology – as well as in clinical and pharmaceutical applications such as infectious diseases, immunology, cancer research, various inherited conditions and drug development.

WGS analyzes (as the name implies) an organism’s entire genome, as opposed to whole exome sequencing and targeted sequencing, which study specific areas. For this reason, WGS is the sequencing option of choice to study factors that affect the entire genome and to analyze noncoding DNA.

De novo sequencing vs resequencing

There are two ways of analyzing whole genome sequencing data: de novo assembly and resequencing.

De novo sequencing offers a way to uncover genome information about microorganisms, animals and plants when no reference genome is available. The analysis works by assembling long parallel phases of genetic material without referencing an existing nucleotide sequence. This type of WGS is highly accurate and can replicate or complete a blueprint for complex or polyploid genomes.

Resequencing a genome involves comparing newly sequenced DNA to a previously created reference genome. It is a highly efficient, fast and cost-effective way of analyzing the genomes of commonly studied organisms. Whole genome resequencing can scan or test for specific genetic variations. Any differences between the sample DNA and the reference could be an indication of a new variant or a potential disorder in a clinical setting.

Library preparation kits

• Illumina TruSeq Nano
• Illumina TruSeq PCR-free
• Illumina Nextera DNA XT
• IDT xGen ssDNA & Low-Input

Sequencing platforms

• Illumina: NovaSeq 6000, HiSeq X, HiSeq 2500, NextSeq 500, MiSeq
• PacBio: Sequel II

Data analysis

Whole genome de novo sequencing

• de novo assembly (long-read sequencing)
• genome survey (K-mer analysis)
• consensus sequence (reads assembled into contigs)
• gene prediction
• gene annotation
• prophage identification

Whole genome resequencing

• alignment (read mapping to reference genome)
• variant calling (SNPs, indels)
• CNV and SV analysis
• tumor–wild type paired analysis
• telomere analysis
• family/trio analysis
• single guide RNA (sgRNA) analysis
• custom mapping, annotations, algorithms and analyses