ArticleGenome biology2022
Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Mapping the evolutionary path towards multi-drug resistance in the pandemicMicrobial genomics · 2026Article
- QCatch: a framework for quality control assessment and analysis of single-cell sequencing data.Bioinformatics (Oxford, England) · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- DVOUG enables robust DNA sequence assembly and reconstruction with a dynamic, variable-order graph.Cell reports methods · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Article
- Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.bioRxiv : the preprint server for biology · 2025Article
- The open-closed mod-minimizer algorithm.Algorithms for molecular biology : AMB · 2025Article
- MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.Bioinformatics (Oxford, England) · 2025Article
- Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3.bioRxiv : the preprint server for biology · 2025Article
- Bioinformatic Methodologies in Assessing Gut Microbiota.Microbiology research · 2024Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets.Bioinformatics (Oxford, England) · 2024Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Fast, parallel, and cache-friendly suffix array construction.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
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
- Compression Algorithm for Colored de Bruijn Graphs.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present Cuttlefish 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17-23 h; and it constructs the graph for 1.52Tbp white spruce reads in approximately 10 h, while the closest competitor requires 54-58 h, using considerably more memory.
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.