Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition

DOI10.4230/LIPICS.WABI.2021.12zbMATH Open1519.92165OpenAlexW3183545999MaRDI QIDQ6133880FDOQ6133880

Authors: Tetsuo Shibuya 

Publication date: 24 July 2023

Full work available at URL: https://doi.org/10.4230/LIPIcs.WABI.2021.12

Recommendations

• Disk compression of \(k\)-mer sets
• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Improved compression of DNA sequencing data with cascading Bloom filters
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• Sparse binary relation representations for genome graph annotation

zbMATH Keywords

compressionde Bruijn graph\(k\)-mersequencing datacolored de Bruijn graph

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cited In (11)

• Disk compression of \(k\)-mer sets
• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Fast approximation of frequent \(k\)-mers and applications to metagenomics
• Eulertigs: minimum plain text representation of \(k\)-mer sets without repetitions in linear time
• Efficient reconciliation of genomic datasets of high similarity
• On weighted \(k\)-mer dictionaries
• Effective parallel multicore-optimized \(k\)-mers counting algorithm
• A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets
• Compression algorithm for colored de Bruijn graphs
• Sparse binary relation representations for genome graph annotation
• Space-Efficient Representation of Genomic k-Mer Count Tables

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