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Assembly gap

Definition
AI-generated

An assembly gap is an unresolved segment in a genome assembly—often represented as Ns or missing coordinates—where reads and consensus sequence do not span repeats, centromeres, or other hard-to-assemble regions.

Topics
Bioinformatics Sequencing Data Analysis
Synonyms
Gap
Related
Consensus sequence De novo assembly Genome assembly

Why it matters in GWAS

Gaps and misassemblies can misplace variants, break LD blocks in local reference panels, and obscure structural variant breakpoints that overlap association credible sets.

Example usage

"The GWAS credible interval spanned an assembly gap on GRCh38, so we checked the T2T-CHM13 alignment."

Consensus sequence De novo assembly Genome assembly N50 Reference genome
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Nurk S, et al. (2022). The complete sequence of a human genome. Science.
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