ArticleBioinformatics (Oxford, England)2017
Succinct colored de Bruijn graphs.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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
51 citing papers in PubMed.
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- IRCAS: a novel end-to-end approach to identify, rectify, and classify comprehensive alternative splicing events in a transcriptome without genome reference.Briefings in bioinformatics · 2026Article
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- A scalable distributed pipeline for reference-free variants calling.BMC genomics · 2025Article
- Metagenomic CRISPR Array Analysis Tool: a novel graph-based approach to finding CRISPR arrays in metagenomic datasets.microLife · 2025Article
- Movi Color: fast and accurate taxonomic classification with the move structure.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
- Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.Genome biology · 2024Article
- Methods for Pangenomic Core Detection.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Pan-genome de Bruijn graph using the bidirectional FM-index.BMC bioinformatics · 2023Article
- WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs.iScience · 2023Article
- Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.Algorithms for molecular biology : AMB · 2023Article
- Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.Bioinformatics (Oxford, England) · 2023Article
- Scalable sequence database search using partitioned aggregated Bloom comb trees.Bioinformatics (Oxford, England) · 2023Article
- Article
- The motif composition of variable number tandem repeats impacts gene expression.Genome research · 2023Article
- Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time.Research square · 2023Article
- Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance.Microbiome · 2022Article
- An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.Bioinformatics (Oxford, England) · 2022Article
- Review
- Data Structures to Represent a Set ofACM computing surveys · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
motivationIn 2012, Iqbal et al. introduced the colored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at 'detecting and genotyping simple and complex genetic variants in an individual or population'. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which requires additional information to be succinctly encoded as well as support for non-standard traversal operations.
resultsOur data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible. AVAILABILITY AND IMPLEMENTATION: https://github.com/cosmo-team/cosmo/tree/VARI. CONTACT: martin.muggli@colostate.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.