ArticleGenome biology2020
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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Who cites it
127 citing papers in PubMed.
- Alignment-freeJournal of clinical microbiology · 2026Article
- AcceleratingProceedings of the National Academy of Sciences of the United States of America · 2026Article
- BiTUGA: scalable prevalence-based unitig association testing for binary traits.G3 (Bethesda, Md.) · 2026Article
- Integrated Genome-Wide Association Study and Machine Learning Approach for Characterizing the Determinants of Biofilm Formation in Staphylococcus aureus.Interdisciplinary sciences, computational life sciences · 2026Article
- A genome-wide association study to identify the genetic loci underlying carbapenem resistance in Acinetobacter baumannii.BMC genomics · 2026Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.Scientific reports · 2026Article
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Empowering global disease surveillance with CURED: a tool for rapid identification of unique genomic biomarkers.mSystems · 2026Article
- Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay.bioRxiv : the preprint server for biology · 2026Article
- Pathological convergence of a bacterial plant pathogen is associated with the horizontal transfer of an effector-containing mobile element.BMC genomics · 2026Article
- AMR-GNN: a multi-representation graph neural network framework to enable genomic antimicrobial resistance prediction.Nature communications · 2026Article
- krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.Genome biology · 2026Article
- Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus.Genome biology · 2026Article
- Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes.Nature microbiology · 2026Article
- Everything is everywhere but Escherichia coli adapts to different niches.The ISME journal · 2026Article
- A comparative genomic approach to identify determinants of meropenem resistance inFrontiers in microbiology · 2026Article
67 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based assemblers reduce the complexity by compacting paths into single vertices, but this is challenging as it requires the uncompacted de Bruijn graph to be available in memory. We present a parallel and memory-efficient algorithm enabling the direct construction of the compacted de Bruijn graph without producing the intermediate uncompacted graph. Bifrost features a broad range of functions, such as indexing, editing, and querying the graph, and includes a graph coloring method that maps each k-mer of the graph to the genomes it occurs in.Availability https://github.com/pmelsted/bifrost.
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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.