Space-Efficient Representation of Genomic k-Mer Count Tables

DOI10.4230/LIPICS.WABI.2021.8zbMATH Open1519.92173OpenAlexW4391336158MaRDI QIDQ6133870FDOQ6133870

Authors: Djamal Belazzougui, Gregory Kucherov 

Publication date: 24 July 2023

Full work available at URL: https://hal.science/hal-03447152

Recommendations

• Disk compression of \(k\)-mer sets
• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition
• Effective parallel multicore-optimized \(k\)-mers counting algorithm
• Succinct de Bruijn graphs

zbMATH Keywords

data structuresminimizerscompressionempirical entropyBloom filter\(k\)-mer countingcompressed static function

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cited In (6)

• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Eulertigs: minimum plain text representation of \(k\)-mer sets without repetitions in linear time
• Fast gapped \(k\)-mer counting with subdivided multi-way bucketed cuckoo hash tables
• On weighted \(k\)-mer dictionaries
• Effective parallel multicore-optimized \(k\)-mers counting algorithm
• Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition

This page was built for publication: Space-Efficient Representation of Genomic k-Mer Count Tables

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q6133870)