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Rainbowfish: A Succinct Colored de Bruijn Graph Representation

https://doi.org/10.1101/138016
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-642-33122-0_18openalex-snapshot
Succinct de Bruijn Graphs
inferredcites →https://doi.org/10.1038/nbt.2862openalex-snapshot
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot
De novo assembly and genotyping of variants using colored de Bruijn graphs
inferredcites →https://doi.org/10.1093/bioinformatics/btx067openalex-snapshot
Succinct colored de Bruijn graphs
inferredcites →https://doi.org/10.1093/nar/gkm965openalex-snapshot
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
inferredcites →https://doi.org/10.1093/nar/gkm978openalex-snapshot
The Rice Annotation Project Database (RAP-DB): 2008 update
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
inferredcites →https://doi.org/10.1109/sfcs.1989.63533openalex-snapshot
Space-efficient static trees and graphs
inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot
The B73 Maize Genome: Complexity, Diversity, and Dynamics
inferredcites →https://doi.org/10.1186/1471-2164-14-791openalex-snapshot
Whole genome resequencing in tomato reveals variation associated with introgression and breeding events
inferredcites →https://doi.org/10.5555/545381.545411openalex-snapshot
Succinct indexable dictionaries with applications to encoding k-ary trees and multisets
inferredcites →https://doi.org/10.7554/elife.13195openalex-snapshot
Resistome diversity in cattle and the environment decreases during beef production

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/imt2.4openalex-snapshot
Applications of de Bruijn graphs in microbiome research
inferred← citeshttps://doi.org/10.1007/978-3-030-00479-8_1openalex-snapshot
Recoloring the Colored de Bruijn Graph
inferred← citeshttps://doi.org/10.1007/978-3-030-17083-7_1openalex-snapshot
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
inferred← citeshttps://doi.org/10.1007/978-3-030-17083-7_8openalex-snapshot
Sparse Binary Relation Representations for Genome Graph Annotation
inferred← citeshttps://doi.org/10.1007/978-3-030-32686-9_22openalex-snapshot
An Index for Sequencing Reads Based on the Colored de Bruijn Graph
inferred← citeshttps://doi.org/10.1007/978-3-030-32686-9_24openalex-snapshot
Space-Efficient Merging of Succinct de Bruijn Graphs
inferred← citeshttps://doi.org/10.1007/s00453-021-00855-2openalex-snapshot
Space Efficient Merging of de Bruijn Graphs and Wheeler Graphs
inferred← citeshttps://doi.org/10.1007/s40484-019-0181-xopenalex-snapshot
Overlap graphs and de Bruijn graphs: data structures for de novogenome assembly in the big data era
inferred← citeshttps://doi.org/10.1016/j.cels.2018.05.021openalex-snapshot
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.06.047openalex-snapshot
Buffering updates enables efficient dynamic de Bruijn graphs
inferred← citeshttps://doi.org/10.1016/j.isci.2019.06.035openalex-snapshot
Sequencing Technologies and Analyses: Where Have We Been and Where Are We Going?
inferred← citeshttps://doi.org/10.1016/j.isci.2020.101224openalex-snapshot
Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ
inferred← citeshttps://doi.org/10.1089/cmb.2019.0322openalex-snapshot
An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search
inferred← citeshttps://doi.org/10.1089/cmb.2019.0324openalex-snapshot
Sparse Binary Relation Representations for Genome Graph Annotation
inferred← citeshttps://doi.org/10.1089/cmb.2022.0259openalex-snapshot
Efficient Colored de Bruijn Graph for Indexing Reads
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf111openalex-snapshot
K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa546openalex-snapshot
Succinct dynamic de Bruijn graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab077openalex-snapshot
Detecting high-scoring local alignments in pangenome graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab281openalex-snapshot
Constructing small genome graphs via string compression
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab408openalex-snapshot
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab749openalex-snapshot
Population-scale detection of non-reference sequence variants using colored de Bruijn graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty632openalex-snapshot
Dynamic compression schemes for graph coloring
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz350openalex-snapshot
Building large updatable colored de Bruijn graphs via merging
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz662openalex-snapshot
Improved representation of sequence bloom trees
inferred← citeshttps://doi.org/10.1093/comjnl/bxx108openalex-snapshot
Relative Suffix Trees
inferred← citeshttps://doi.org/10.1101/2020.10.01.322164openalex-snapshot
Indexing All Life’s Known Biological Sequences
inferred← citeshttps://doi.org/10.1101/2021.02.05.429839openalex-snapshot
An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees
inferred← citeshttps://doi.org/10.1101/2023.05.12.540616openalex-snapshot
Compression algorithm for colored de Bruijn graphs
inferred← citeshttps://doi.org/10.1101/2025.02.02.636161openalex-snapshot
Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3
inferred← citeshttps://doi.org/10.1101/2025.05.22.655637openalex-snapshot
Movi Color: fast and accurate long-read classification with the move structure
inferred← citeshttps://doi.org/10.1101/217372openalex-snapshot
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
inferred← citeshttps://doi.org/10.1101/236711openalex-snapshot
Metannot: A succinct data structure for compression of colors in dynamic de Bruijn graphs
inferred← citeshttps://doi.org/10.1101/gr.260604.119openalex-snapshot
Data structures based on k -mers for querying large collections of sequencing data sets
inferred← citeshttps://doi.org/10.1109/tcbb.2017.2737999openalex-snapshot
FastEtch: A Fast Sketch-Based Assembler for Genomes
inferred← citeshttps://doi.org/10.1145/3445967openalex-snapshot
Data Structures to Represent a Set of k -long DNA Sequences
inferred← citeshttps://doi.org/10.1145/3571723openalex-snapshot
Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond
inferred← citeshttps://doi.org/10.1145/3765612.3767233openalex-snapshot
Movi Color: fast and accurate taxonomic classification with the move structure
inferred← citeshttps://doi.org/10.1177/15578666261416557openalex-snapshot
USTAR-CR: Efficient and Compact Compression of k -Mer Sets Through Colored de Bruijn Graphs
inferred← citeshttps://doi.org/10.1186/s12859-021-04149-wopenalex-snapshot
A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes
inferred← citeshttps://doi.org/10.1186/s13015-020-00164-3openalex-snapshot
Alignment- and reference-free phylogenomics with colored de Bruijn graphs
inferred← citeshttps://doi.org/10.1186/s13059-020-02135-8openalex-snapshot
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
inferred← citeshttps://doi.org/10.1186/s13059-020-02168-zopenalex-snapshot
The design and construction of reference pangenome graphs with minigraph
inferred← citeshttps://doi.org/10.1186/s13059-020-02237-3openalex-snapshot
BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
inferred← citeshttps://doi.org/10.1186/s13059-021-02442-8openalex-snapshot
VariantStore: an index for large-scale genomic variant search
inferred← citeshttps://doi.org/10.3389/fgene.2023.1250907openalex-snapshot
Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs
inferred← citeshttps://doi.org/10.3929/ethz-b-000236144openalex-snapshot
Efficient graph-color compression with neighborhood-informed Bloom filters
inferred← citeshttps://doi.org/10.48550/arxiv.1806.01799openalex-snapshot
Survey and Taxonomy of Lossless Graph Compression and Space-Efficient Graph Representations
inferred← citeshttps://doi.org/10.48550/arxiv.1809.07320openalex-snapshot
Compressing and Indexing Aligned Readsets
inferred← citeshttps://doi.org/10.48550/arxiv.2003.06079openalex-snapshot
The design and construction of reference pangenome graphs
inferred← citeshttps://doi.org/10.64898/2026.02.16.706153openalex-snapshot
Construction of distinct k -mer color sets via set fingerprinting
inferred← citeshttps://doi.org/10.64898/2026.08.26.747224openalex-snapshot
Dynamic Hierarchical Interleaved Bloom Filter: An Updatable Index for Large-Scale Fast Sequence Search
inferred← citeshttps://doi.org/10.70675/a61f77f4z0662z41e2z8db6zc2604537b1c1openalex-snapshot
Sketch-based approaches to process massive string data
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