A tale of optimizing the space taken by de Bruijn graphs

DOI10.1007/978-3-030-80049-9_11MaRDI QIDQ2117772zbMATH OpenOpenAlexFDO

Authors Rayan Chikhi

Publication date 22 March 2022

Full work available at URL https://doi.org/10.1007/978-3-030-80049-9_11

zbMATH Keywords

data structuresbioinformaticsde Bruijn graphs

Mathematics Subject Classification ID

Theory of computing (68Qxx)

Recommendations

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Cites work

• Disk compression of \(k\)-mer sets
• Dynamic alignment-free and reference-free read compression
• Fast and scalable minimal perfect hashing for massive key sets
• Hierarchical overlap graph
• Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
• Succinct de Bruijn graphs

Describes a project that uses

Uses Software

• SPAdes
• Velvet
• ABySS
• MEGAHIT
• DARRC
• Salmon
• IDBA

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