ArticleNature methods2022
Long-read mapping to repetitive reference sequences using Winnowmap2.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 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
187 citing papers in PubMed, 271 citations in OpenAlex.
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- Genomic structural variation rescues a classic biological invader from a population bottleneck.Science advances · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Revisiting HPV integration landscapes using telomere-to-telomere human genome reference closes the gaps in HPV integration sites search.Virology journal · 2026Article
- Complete chromosome 21 centromere sequencing of families with Down syndrome.American journal of human genetics · 2026Article
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- Telomere-to-telomere genome of Stylosanthes guianensis uncovers symbiotic adaptation to phosphorus-deficient soils.Genome biology · 2026Article
- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis.bioRxiv : the preprint server for biology · 2026Article
- A new integrated genetic and transcriptomic approach for investigating DUX4 and DUX4C.Journal of human genetics · 2026Article
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- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
127 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.