ArticleBioinformatics (Oxford, England)2021
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 38 citations in OpenAlex.
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- AlfaPang: alignment free algorithm for pangenome graph construction.Algorithms for molecular biology : AMB · 2025Article
- Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3.bioRxiv : the preprint server for biology · 2025Article
- Graphite: painting genomes using a colored de Bruijn graph.NAR genomics and bioinformatics · 2024Article
- Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.Genome research · 2024Article
- Space-efficient computation of k-mer dictionaries for large values of k.Algorithms for molecular biology : AMB · 2024Article
- Fulgor: a fast and compact k-mer index for large-scale matching and color queries.Algorithms for molecular biology : AMB · 2024Article
- KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2024Article
- simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry.Bioinformatics (Oxford, England) · 2023Article
- Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.Genome research · 2023Article
- Locality-preserving minimal perfect hashing of k-mers.Bioinformatics (Oxford, England) · 2023Article
- Fulgor: A fast and compactbioRxiv : the preprint server for biology · 2023Article
- simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry.bioRxiv : the preprint server for biology · 2023Article
- Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing.bioRxiv : the preprint server for biology · 2023Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
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2 authors at 1 institution in 1 country.
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Abstract
motivationThe construction of the compacted de Bruijn graph from collections of reference genomes is a task of increasing interest in genomic analyses. These graphs are increasingly used as sequence indices for short- and long-read alignment. Also, as we sequence and assemble a greater diversity of genomes, the colored compacted de Bruijn graph is being used more and more as the basis for efficient methods to perform comparative genomic analyses on these genomes. Therefore, time- and memory-efficient construction of the graph from reference sequences is an important problem.
resultsWe introduce a new algorithm, implemented in the tool Cuttlefish, to construct the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel approach of modeling de Bruijn graph vertices as finite-state automata, and constrains these automata's state-space to enable tracking their transitioning states with very low memory usage. Cuttlefish is also fast and highly parallelizable. Experimental results demonstrate that it scales much better than existing approaches, especially as the number and the scale of the input references grow. On a typical shared-memory machine, Cuttlefish constructed the graph for 100 human genomes in under 9 h, using ∼29 GB of memory. On 11 diverse conifer plant genomes, the compacted graph was constructed by Cuttlefish in under 9 h, using ∼84 GB of memory. The only other tool completing these tasks on the hardware took over 23 h using ∼126 GB of memory, and over 16 h using ∼289 GB of memory, respectively. AVAILABILITY AND IMPLEMENTATION: Cuttlefish is implemented in C++14, and is available under an open source license at https://github.com/COMBINE-lab/cuttlefish. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.