ArticleGigaScience2025
Challenges in structural variant calling in low-complexity regions.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed.
- Improving Long-Read Somatic Structural Variant Calling with Pangenome and De Novo Personal Genome Assembly.Cancer research communications · 2026Article
- Article
- Short-Read Sequencing Benchmarking with Donor-Specific Assemblies.bioRxiv : the preprint server for biology · 2026Article
- Finding low-complexity DNA sequences with longdust.Bioinformatics (Oxford, England) · 2026Article
- Efficient near telomere-to-telomere assembly of Nanopore Simplex reads.bioRxiv : the preprint server for biology · 2025Article
- Article
- SVUPP: Pre-phasing long reads improves structural variant genotyping.Bioinformatics (Oxford, England) · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundStructural variants (SVs) are genomic differences $\ge$50 bp in length. They remain challenging to detect, even with long-sequence reads, and the sources of these difficulties are not well quantified.
resultsWe identified 35.4 Mb of low-complexity regions (LCRs) in GRCh38. Although these regions cover only 1.2% of the genome, they contain 69.1% of confident SVs in sample HG002. Across long-read SV callers, 77.3-91.3% of erroneous SV calls occur within LCRs, with error rates increasing with LCR length.
conclusionSVs are enriched and difficult to call in LCRs. Special care needs to be taken for calling and analyzing these variants.
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