Resequence

Resequence, or resequencing, in genomics refers to sequencing the genome of an organism or specific genomic regions that have previously been sequenced, in order to detect genetic variation relative to a reference genome. It contrasts with de novo sequencing, which builds a genome assembly from scratch. Resequencing is widely used to characterize natural or experimental variation, including single-nucleotide polymorphisms (SNPs), insertions and deletions (indels), and larger structural variants.

The typical workflow involves obtaining DNA samples, performing high-throughput sequencing, and mapping the resulting reads to a reference genome. Variant calling identifies differences between the sequenced sample and the reference, followed by filtering, quality control, and annotation to estimate potential functional effects. Depending on goals, approaches may include whole-genome resequencing for broad surveys or targeted resequencing to cover genes, exons, or regions of interest. Data analysis often requires population genetics tools to infer allele frequencies, haplotypes, and population structure.

Applications of resequencing include population genomics to study diversity and evolutionary history, medical and pharmacogenomic research to identify disease-associated variants, and agricultural genomics to improve crops and livestock through marker-assisted selection. Resequencing is also used in microbial genomics for outbreak tracing and resistance gene discovery.

Challenges include reference bias, sequencing errors, uneven coverage, and difficulty accurately calling variants in repetitive or structurally complex regions. Costs have decreased with advancing sequencing technologies, making resequencing a routine tool in genetics and genomics.