ArticleCell systems2021
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.
Article in Cell systems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
65 citing papers in PubMed.
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- LCPAN: efficient variation graph construction using locally consistent parsing.Genome biology · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- DVOUG enables robust DNA sequence assembly and reconstruction with a dynamic, variable-order graph.Cell reports methods · 2025Article
- Density-reducing Jaccard estimators for sketch-based long read applications.BMC bioinformatics · 2025Article
- Robust 16S rRNA classification based on a compressed LCA index.Genome research · 2025Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- Oatk: a de novo assembly tool for complex plant organelle genomes.Genome biology · 2025Article
- Fast and flexible minimizer digestion with digest.Bioinformatics (Oxford, England) · 2025Article
- Review
- Sequence similarity estimation by random subsequence sketching.bioRxiv : the preprint server for biology · 2025Article
- TopoQual polishes circular consensus sequencing data and accurately predicts quality scores.BMC bioinformatics · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Faster run-length compressed suffix arrays.Oasics : openaccess series in informatics · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
3 authors.
Funding
Abstract
DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of minimizer-space de Bruijn graphs to enable long-read genome assembly. mdBG achieves orders-of-magnitude improvement in both speed and memory usage over existing methods without compromising accuracy. A human genome is assembled in under 10 min using 8 cores and 10 GB RAM, and 60 Gbp of metagenome reads are assembled in 4 min using 1 GB RAM. In addition, we constructed a minimizer-space de Bruijn graph-based representation of 661,405 bacterial genomes, comprising 16 million nodes and 45 million edges, and successfully search it for anti-microbial resistance (AMR) genes in 12 min. We expect our advances to be essential to sequence analysis, given the rise of long-read sequencing in genomics, metagenomics, and pangenomics. Code for constructing mdBGs is freely available for download at https://github.com/ekimb/rust-mdbg/.
Indexed as
Identifiers
What OpenQuestion holds
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.