Bloom filter trie -- a data structure for pan-genome storage

DOI10.1007/978-3-662-48221-6_16MaRDI QIDQ5283830zbMATH OpenOpenAlexFDO

Authors Guillaume Holley, Roland Wittler, Jens Stoye

Publication date 25 July 2017

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

Full work available at URL https://doi.org/10.1007/978-3-662-48221-6_16

zbMATH Keywords

Bloom filter triecolored de-Bruijn graph

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Data structures (68P05) Computational methods for problems pertaining to biology (92-08)

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Cites work

• An experimental study of an opportunistic index
• PanCake: a data structure for pangenomes
• Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
• Space/time trade-offs in hash coding with allowable errors

Cited in

(6)

• Rainbowfish: a succinct colored de Bruijn graph representation
• PanCake: a data structure for pangenomes
• Representation of \(k\)-mer sets using spectrum-preserving string sets
• Dynamic alignment-free and reference-free read compression
• An index for sequencing reads based on the colored de Bruijn graph
• Efficient construction of a compressed de Bruijn graph for pan-genome analysis

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