Representation of k-mer sets using spectrum-preserving string sets

DOI10.1007/978-3-030-45257-5_10MaRDI QIDQ5041804zbMATH OpenOpenAlexFDO

Authors Amatur Rahman, Paul Medvedev

Publication date 14 October 2022

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-030-45257-5_10

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
• Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition
• Space-Efficient Representation of Genomic k-Mer Count Tables
• Succinct de Bruijn graphs

Cites work

• \textit{De novo} clustering of long-read transcriptome data using a greedy, quality-value based algorithm
• Bidirectional variable-order de Bruijn graphs
• Bloom filter trie -- a data structure for pan-genome storage
• Fully dynamic de Bruijn graphs
• scientific article; zbMATH DE number 2203240 (Why is no real title available?)
• Succinct de Bruijn graphs

Cited in

(6)

• Spectrum preserving tilings enable sparse and modular reference indexing
• Space-Efficient Representation of Genomic k-Mer Count Tables
• Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition
• 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

Describes a project that uses

Uses Software

• deGSM
• KMC
• GitHub

This page was built for publication: Representation of \(k\)-mer sets using spectrum-preserving string sets

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5041804)