Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition

DOI10.4230/LIPICS.WABI.2021.12MaRDI QIDQ6133880zbMATH OpenOpenAlexFDO

Authors Tetsuo Shibuya

Publication date 24 July 2023

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

zbMATH Keywords

\(k\)-mercolored de Bruijn graphcompressionde Bruijn graphsequencing data

Mathematics Subject Classification ID

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

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
• Space-Efficient Representation of Genomic k-Mer Count Tables
• Sparse binary relation representations for genome graph annotation

Cited in

(11)

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

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