ArticleNature genetics2012
De novo assembly and genotyping of variants using colored de Bruijn graphs.
Article in Nature genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 320 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
320 citing papers in PubMed.
- Validation of an optimized Oxford Nanopore sequencing workflow versus Illumina for mycobacteria from primary MGIT culture.Microbiology spectrum · 2026Article
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens.The Plant journal : for cell and molecular biology · 2026Review
- UShER-TB: scalable, comprehensive, accessible phylogenomic analysis ofMicrobial genomics · 2026Article
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs.NAR genomics and bioinformatics · 2026Article
- GrassSV - hybrid method to detect structural variants in high throughput DNA-seq data.PLoS computational biology · 2026Article
- Article
- bronko: ultrafast, alignment-free detection of viral genome variation.bioRxiv : the preprint server for biology · 2026Article
- Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663Microbial genomics · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
- Article
- UShER-TB: Scalable, Comprehensive, Accessible Phylogenomic Analysis ofmedRxiv : the preprint server for health sciences · 2025Article
- A scalable distributed pipeline for reference-free variants calling.BMC genomics · 2025Article
- Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Pseudoassembly of k-mers.bioRxiv : the preprint server for biology · 2025Article
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
260 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.
Funding
Abstract
Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We provide an efficient software implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic genomes simultaneously. Four applications of Cortex are presented. First, we detect and validate both simple and complex structural variations in a high-coverage human genome. Second, we identify more than 3 Mb of sequence absent from the human reference genome, in pooled low-coverage population sequence data from the 1000 Genomes Project. Third, we show how population information from ten chimpanzees enables accurate variant calls without a reference sequence. Last, we estimate classical human leukocyte antigen (HLA) genotypes at HLA-B, the most variable gene in the human genome.
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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.