Nothing Special   »   [go: up one dir, main page]

Shibuya et al., 2022 - Google Patents

Space-efficient representation of genomic k-mer count tables

Shibuya et al., 2022

View HTML @Full View
Document ID
2397975122627600618
Author
Shibuya Y
Belazzougui D
Kucherov G
Publication year
Publication venue
Algorithms for Molecular Biology

External Links

Snippet

Motivation k-mer counting is a common task in bioinformatic pipelines, with many dedicated tools available. Many of these tools produce in output k-mer count tables containing both k- mers and counts, easily reaching tens of GB. Furthermore, such tables do not support …
Continue reading at link.springer.com (HTML) (other versions)

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30312—Storage and indexing structures; Management thereof
    • G06F17/30321—Indexing structures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30386—Retrieval requests
    • G06F17/30424—Query processing
    • G06F17/30442—Query optimisation
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30067—File systems; File servers
    • G06F17/30129—Details of further file system functionalities
    • G06F17/3015—Redundancy elimination performed by the file system
    • G06F17/30156—De-duplication implemented within the file system, e.g. based on file segments
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30587—Details of specialised database models
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30943—Information retrieval; Database structures therefor; File system structures therefor details of database functions independent of the retrieved data type
    • G06F17/30946—Information retrieval; Database structures therefor; File system structures therefor details of database functions independent of the retrieved data type indexing structures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/3061—Information retrieval; Database structures therefor; File system structures therefor of unstructured textual data
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30017—Multimedia data retrieval; Retrieval of more than one type of audiovisual media
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/3074—Audio data retrieval
    • G06F17/30778—Audio database index structures and management thereof
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/20—Handling natural language data
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/62—Protecting access to data via a platform, e.g. using keys or access control rules
    • G06F21/6218—Protecting access to data via a platform, e.g. using keys or access control rules to a system of files or objects, e.g. local or distributed file system or database
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F9/00—Arrangements for programme control, e.g. control unit
    • G06F9/06—Arrangements for programme control, e.g. control unit using stored programme, i.e. using internal store of processing equipment to receive and retain programme
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F7/00—Methods or arrangements for processing data by operating upon the order or content of the data handled

Similar Documents

Publication Publication Date Title
Holley et al. Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
Pandey et al. Mantis: a fast, small, and exact large-scale sequence-search index
Erbert et al. Gerbil: a fast and memory-efficient k-mer counter with GPU-support
Bingmann et al. COBS: a compact bit-sliced signature index
Lemire et al. SIMD compression and the intersection of sorted integers
Shibuya et al. Space-efficient representation of genomic k-mer count tables
Holley et al. Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
Harris et al. Improved representation of sequence bloom trees
Wang et al. Scimate: A novel mapreduce-like framework for multiple scientific data formats
Deorowicz FQSqueezer: k-mer-based compression of sequencing data
Ahmadi et al. Hobbes: optimized gram-based methods for efficient read alignment
Sahlin Strobealign: flexible seed size enables ultra-fast and accurate read alignment
Wandelt et al. Adaptive efficient compression of genomes
Rowe When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data
Gürsoy et al. Storing and analyzing a genome on a blockchain
Wang et al. CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table
Ferraro Petrillo et al. Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
Pibiri On weighted k-mer dictionaries
Holley et al. Bloom filter trie–a data structure for pan-genome storage
Rahman et al. Disk compression of k-mer sets
Yan et al. Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method
Liu et al. GPU-accelerated BWT construction for large collection of short reads
Schmidt et al. Matchtigs: minimum plain text representation of k-mer sets
Shiryev et al. Indexing and searching petabase-scale nucleotide resources
Nayak et al. A review on role of bloom filter on dna assembly