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Data Structures to Represent a Set of k -long DNA Sequences
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Introduction to Algorithms
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An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
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COBS: A Compact Bit-Sliced Signature Index
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On the Representation of de Bruijn Graphs
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Fully Dynamic de Bruijn Graphs
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Computability of Models for Sequence Assembly
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Hash, Displace, and Compress
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Succinct de Bruijn Graphs
inferredcites →https://doi.org/10.1007/978-3-642-33122-0_19openalex-snapshot
Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter
inferredcites →https://doi.org/10.1007/978-3-642-38036-5_24openalex-snapshot
Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data
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Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs
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Bidirectional Variable-Order de Bruijn Graphs
inferredcites →https://doi.org/10.1016/j.cels.2018.05.021openalex-snapshot
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index
inferredcites →https://doi.org/10.1016/j.csl.2009.12.001openalex-snapshot
Recursive n-gram hashing is pairwise independent, at best
inferredcites →https://doi.org/10.1016/j.dam.2018.03.035openalex-snapshot
A resource-frugal probabilistic dictionary and applications in bioinformatics
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Bloofi: Multidimensional Bloom filters
inferredcites →https://doi.org/10.1016/j.tcs.2012.02.002openalex-snapshot
Lightweight algorithms for constructing and inverting the BWT of string collections
inferredcites →https://doi.org/10.1016/j.ymeth.2016.02.020openalex-snapshot
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
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Genome-Scale Algorithm Design
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Fast search of thousands of short-read sequencing experiments
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De novo assembly and genotyping of variants using colored de Bruijn graphs
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Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
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Ultrafast search of all deposited bacterial and viral genomic data
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Network Applications of Bloom Filters: A Survey
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A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1089/cmb.2016.0155openalex-snapshot
Improving Bloom Filter Performance on Sequence Data Using k -mer Bloom Filters
inferredcites →https://doi.org/10.1089/cmb.2017.0265openalex-snapshot
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees
inferredcites →https://doi.org/10.1089/cmb.2020.0431openalex-snapshot
Representation of k -Mer Sets Using Spectrum-Preserving String Sets
inferredcites →https://doi.org/10.1093/bioinformatics/bth408openalex-snapshot
Reducing storage requirements for biological sequence comparison
inferredcites →https://doi.org/10.1093/bioinformatics/btq230openalex-snapshot
Classification of DNA sequences using Bloom filters
inferredcites →https://doi.org/10.1093/bioinformatics/btq697openalex-snapshot
Succinct data structures for assembling large genomes
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Compacting de Bruijn graphs from sequencing data quickly and in low memory
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Succinct colored de Bruijn graphs
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deBGR: an efficient and near-exact representation of the weighted de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/btx432openalex-snapshot
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures
inferredcites →https://doi.org/10.1093/bioinformatics/btx636openalex-snapshot
Squeakr: an exact and approximate k -mer counting system
inferredcites →https://doi.org/10.1093/bioinformatics/bty292openalex-snapshot
A space and time-efficient index for the compacted colored de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/bty632openalex-snapshot
Dynamic compression schemes for graph coloring
inferredcites →https://doi.org/10.1093/bioinformatics/btz662openalex-snapshot
Improved representation of sequence bloom trees
inferredcites →https://doi.org/10.1101/138016openalex-snapshot
Rainbowfish: A Succinct Colored de Bruijn Graph Representation
inferredcites →https://doi.org/10.1101/434795openalex-snapshot
Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters
inferredcites →https://doi.org/10.1101/gr.214346.116openalex-snapshot
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
inferredcites →https://doi.org/10.1101/gr.260604.119openalex-snapshot
Data structures based on k -mers for querying large collections of sequencing data sets
inferredcites →https://doi.org/10.1109/90.851975openalex-snapshot
Summary cache: a scalable wide-area Web cache sharing protocol
inferredcites →https://doi.org/10.1109/dcc.2005.13openalex-snapshot
An Extension of the Burrows Wheeler Transform to k Words
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Opportunistic data structures with applications
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Theory and Practice of Bloom Filters for Distributed Systems
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Fast de Bruijn Graph Compaction in Distributed Memory Environments
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Practical Entropy-Compressed Rank/Select Dictionary
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Cost-optimal assignment of elements in genome-scale multi-way bucketed Cuckoo hash tables
inferredcites →https://doi.org/10.1145/1240233.1240243openalex-snapshot
Compressed representations of sequences and full-text indexes
inferredcites →https://doi.org/10.1145/1290672.1290680openalex-snapshot
Succinct indexable dictionaries with applications to encoding k -ary trees, prefix sums and multisets
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Compressing and indexing labeled trees, with applications
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Fully Functional Static and Dynamic Succinct Trees
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A General-Purpose Counting Filter
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Efficient Storage and Retrieval by Content and Address of Static Files
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Space/time trade-offs in hash coding with allowable errors
inferredcites →https://doi.org/10.1146/annurev-genom-090314-050032openalex-snapshot
The Theory and Practice of Genome Sequence Assembly
inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12859-016-1103-9openalex-snapshot
Read mapping on de Bruijn graphs
inferredcites →https://doi.org/10.1186/s13015-016-0066-8openalex-snapshot
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
inferredcites →https://doi.org/10.1186/s13059-018-1535-9openalex-snapshot
SeqOthello: querying RNA-seq experiments at scale
inferredcites →https://doi.org/10.1186/s13059-020-02135-8openalex-snapshot
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
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Simplitigs as an efficient and scalable representation of de Bruijn graphs
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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findere: Fast and Precise Approximate Membership Query
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Engineering a Textbook Approach to Index Massive String Dictionaries
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Expected Density of Random Minimizers
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A Linear Algorithm For Efficient Representation of k-mer Sets Using De Bruijn Graphs
inferred← citeshttps://doi.org/10.1007/978-3-032-02489-3_5openalex-snapshot
Fast and Succinct Compression of k-mer Sets with Plain Text Representation of Colored de Bruijn Graphs
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Minimizers in Semi-dynamic Strings
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Genome-Wide Copy Number Variation and Structural Variation: A Novel Tool for Improved Livestock Genomic Selection
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USTAR: Improved Compression of k-mer Sets with Counters Using de Bruijn Graphs
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Dynamic Label Assignment in Deep Learning Object Detection: A Comprehensive Survey and Unified Computational Framework
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A blockchain-based application for genomic access and variant discovery using smart contracts and homomorphic encryption
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Two-level massive string dictionaries
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Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA
inferred← citeshttps://doi.org/10.1089/cmb.2024.0530openalex-snapshot
Enhanced Compression of k -Mer Sets with Counters via de Bruijn Graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab309openalex-snapshot
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac245openalex-snapshot
Sparse and skew hashing of K-mers
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac528openalex-snapshot
The K-mer File Format: a standardized and compact disk representation of sets ofk-mers
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac734openalex-snapshot
Syllable-PBWT for space-efficient haplotype long-match query
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad305openalex-snapshot
fimpera: drastic improvement of Approximate Membership Query data-structures with counts
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae217openalex-snapshot
Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf054openalex-snapshot
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data
inferred← citeshttps://doi.org/10.1101/2021.05.31.446182openalex-snapshot
findere: fast and precise approximate membership query
inferred← citeshttps://doi.org/10.1101/2024.03.06.583483openalex-snapshot
Towards Efficient k- Mer Set Operations via Function-Assigned Masked Superstrings
inferred← citeshttps://doi.org/10.1101/2024.10.30.621029openalex-snapshot
FroM Superstring to Indexing: a space-efficient index for unconstrained k -mer sets using the Masked Burrows-Wheeler Transform (MBWT)
inferred← citeshttps://doi.org/10.1101/2025.07.10.664199openalex-snapshot
Efficiency of Learned Indexes on Genome Spectra
inferred← citeshttps://doi.org/10.1101/gr.277615.122openalex-snapshot
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
inferred← citeshttps://doi.org/10.1101/gr.281453.125openalex-snapshot
Hash functions in nucleotide sequence analysis
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On Nonlinear Learned String Indexing
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Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond
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Grafite: Taming Adversarial Queries with Optimal Range Filters
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Aeris Filter: A Strongly and Monotonically Adaptive Range Filter
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Zeno Filter: To Infinity in Tiny Steps
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USTAR-CR: Efficient and Compact Compression of k -Mer Sets Through Colored de Bruijn Graphs
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Fast, parallel, and cache-friendly suffix array construction
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Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
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When less is more: sketching with minimizers in genomics
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SFQ: Constructing and Querying a Succinct Representation of FASTQ Files
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Порівняння представлень k-мер-даних ДНК для класифікації через нейронні мережі
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Design and implementation of bioinformatic tools for RNA sequencing data analysis
inferred← citeshttps://doi.org/10.70675/ac967d12zc0a7z4126z92aez5b8e41949671openalex-snapshot
Indexation et analyse de grandes collections de séquençages via des matrices de k-mers
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