ArticleNature methods2024
Improved sequence mapping using a complete reference genome and lift-over.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Using pangenome variation graphs to improve mutation detection in a large DNA virus.Microbial genomics · 2026Article
- CrossFilt: a cross-species filtering tool that eliminates alignment bias in comparative genomics studies of primates.Genome biology · 2026Article
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- Choose your human genome reference wisely.Nature methods · 2025Article
- Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.Genome research · 2025Article
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation.bioRxiv : the preprint server for biology · 2025Article
- Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.Communications biology · 2024Article
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.Nature methods · 2024Article
- What's in a method name?Nature methods · 2024Article
- Measuring, visualizing, and diagnosing reference bias with biastools.Genome biology · 2024Article
- The benefit of a complete reference genome for cancer structural variant analysis.medRxiv : the preprint server for health sciences · 2024Article
- Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review.NPJ genomic medicine · 2024Review
- Measuring, visualizing and diagnosing reference bias with biastools.bioRxiv : the preprint server for biology · 2024Article
- A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.PloS one · 2024Article
- Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a method called levioSAM2 that performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of several references, we demonstrate that aligning reads to a high-quality reference (for example, T2T-CHM13) and lifting to an older reference (for example, Genome reference Consortium (GRC)h38) improves the accuracy of the resulting variant calls on the old reference. By leveraging the quality improvements of T2T-CHM13, levioSAM2 reduces small and structural variant calling errors compared with GRC-based mapping using real short- and long-read datasets. Performance is especially improved for a set of complex medically relevant genes, where the GRC references are lower quality.
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