Whole Genome Sequencing

Whole Genome Sequencing (WGS) is the process of determining the complete nucleotide sequence of an organism’s genome in a single experiment ¹.

How It Works

Genomic DNA is extracted, fragmented, and prepared into sequencing libraries with platform-specific adapters. Short-read platforms such as Illumina produce reads of 150-300 base pairs with high accuracy and throughput. Long-read platforms like PacBio and Oxford Nanopore generate reads exceeding 10 kilobases, improving assembly across repetitive regions and structural variants.

Reads are either aligned to a reference genome for resequencing applications or assembled de novo when no reference exists. Sufficient depth of coverage (typically 30x or more for variant calling) ensures reliable detection of single-nucleotide variants, insertions, deletions, and structural rearrangements.

In synthetic biology, WGS verifies engineered strain genotypes, detects off-target mutations introduced during genome editing, confirms pathway integration sites, and monitors genomic stability during adaptive laboratory evolution experiments.

Computational Considerations

WGS data analysis pipelines typically follow the GATK best practices workflow: read alignment with BWA-MEM, duplicate marking, base quality score recalibration, and variant calling with HaplotypeCaller ². Structural variant detection requires specialized tools such as Manta or Delly. Annotation pipelines (SnpEff, VEP) predict functional consequences of identified variants. For engineered organisms, custom pipelines map reads against designed construct sequences to verify correct assembly and integration.

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