Whole Genome Sequencing is a comprehensive sequencing method for determining an organism's complete genome sequence. It enables analysis of the entire DNA complement, whether derived from bacteria, plants, animals or humans.

WGS Workflow

01DNA extraction: Collection of a sample (e.g. blood, saliva, tissue, or microorganisms) followed by DNA extraction.

02Library preparation: DNA fragmentation and addition of sequencing adapters and indexes.

03Sequencing: Sequencing on Illumina, PacBio, or ONT (Oxford Nanopore Technologies) platforms.

04Bioinformatics analysis: Genome assembly to reconstruct the whole-genome sequence from short reads, followed by gene annotation and comparison with a reference genome.

WGS workflow diagram - from sample to results

Applications of WGS:

01Medical genetics:

Diagnosis of genetic disorders, including the identification of disease-associated variants in rare and multifactorial conditions.
Personalised medicine - tailoring treatment to an individual's genetic profile.

02Oncology research:

Analysis of somatic variants in tumours.
Identification of structural variants, including translocations.

03Microbiology and epidemiology:

Pathogen identification and characterisation.
Outbreak tracing.

04Biotechnology and agriculture:

Characterisation of plant and livestock genomes.
Development of new crop varieties and animal breeds.

05Evolutionary and ecological research:

Analysis of genetic diversity and organismal phylogeny.
Investigation of adaptation and speciation.

WGS service options

Human WGS
Resequencing WGS (plants/animals) using a reference genome
de novo WGS - no reference genome available
Hi-C -based genome assembly

Technical specifications for WGS:

Sequencing mode:
- Illumina: 2 x 150 bp
- ONT: 8kb or 100kb reads for de novo WGS
- PacBio Revio: 15 kb HiFi
Recommended genome coverage / amount of data per sample:
- Human WGS and resequencing WGS
  - MGI DNBSEQ-T7: ≥ 30 X
  - Nanopore PromethION 48: ≥ 30 X
  - PacBio Revio: ≥ 10 X
- de novo WGS - a multiplatform approach is recommended, comprising:
  - Genome Survey: Illumina NovaSeq: ≥ 50 X
  - PacBio Revio genome sequencing: ≥ 30X
  - Gap Filling: Nanopore PromethION 48 (read length 100 kb): ≥ 40 X
  - Hi-C: Illumina NovaSeq: ≥ 100 X
- Hi-C -based genome assembly
  - Hi-C: Illumina NovaSeq: ≥ 100 X

Sample Requirements

Minimum Sample Requirements - DNA/RNA (Illumina):

Sample type: gDNA
Amount: > 500 ng
Concentration (NanoDrop): >20 ng/μL
Volume: >20 μL
Purity (OD260/280): 1.7 - 2.2

Minimum Sample Requirements - DNA/RNA (PacBio):

Sample type: gDNA
Amount: > 10μg
Concentration (NanoDrop): >50 ng/μL
Volume: >20 μL
Purity (OD260/280): 1.7 - 2.2

Minimum Sample Requirements - DNA/RNA (ONT):

Sample type: gDNA
Amount: > 4μg
Concentration (NanoDrop): >50 ng/μL
Volume: >20 μL
Purity (OD260/280): 1.7 - 2.2

We recommend submitting samples at quantities and concentrations above the minimum requirements.

IMPORTANT

We recommend submitting at least 2 samples (1 g each) for the Hi-C -based genome assembly experiment, which includes DNA extraction.

All samples submitted for de novo WGS should originate from the same individual. RNA-seq (Illumina) is required for genome annotation. We recommend pooling samples collected from different tissues and time points.

DNA extraction from submitted samples is also available. Details here.

WGS Bioinformatics Analysis

Human WGS
- Post-sequencing data quality control
- Alignment to the reference genome
- SNP identification and annotation
- Small indel identification and annotation
- SV and CNV identification and annotation (for long-read sequencing or high sequencing depth only)
- Genome-wide distribution of variants
- Functional annotation of variants (NR, SwissProt, GO, KEGG, COG, KOG, Pfam)
WGS resequencing
- Post-sequencing data quality control
- Alignment to the reference genome
- SNP identification and annotation
- Small indel identification and annotation
- SV and CNV identification and annotation
- Genome-wide distribution of variants
- Nonsynonymous variants
- Functional annotation of genes containing variants
de novo WGS
- Genome Survey:
  - Estimation of genome size
  - Estimation of genome heterozygosity, repeat content, and GC content
- Genome assembly de novo:
  - Raw data processing and quality assessment
  - Genome assembly
- Genome annotation
  - Whole-genome annotation:
    - Protein-coding genes, repetitive sequences, transposable elements, non-coding RNAs, and pseudogenes
  - Functional annotation:
    - NR, eggNOG, GO, KEGG, TrEMBL, Swiss-Prot, Pfam, InterPro
- Assembly based on Hi-C
  - Data processing and quality assessment, including library evaluation using Hi-C
  - Scaffolding contigs using Hi-C
  - Assembly quality assessment

Example Figures

Example plots from a WGS bioinformatics analysis report

Comparison: Illumina vs AVITI Metatranscriptomics or prokaryotic RNA-seq: which should you choose?Whole Exome Sequencing SLAF-seq Whole Bacterial/Fungal Genome Sequencing GENOMICS

KEYWORDS

WGSwhole-genome sequencingfull genome sequencingcomplete genome sequencingresequencingde novoreference genomegenome sequencingHuman WGSPlant & Animal WGS

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Whole Genome Sequencing (WGS)