Rainbowfish: a succinct colored de Bruijn graph representation

DOI10.4230/LIPICS.WABI.2017.18MaRDI QIDQ5111820zbMATHOpenAlexFDO

Authors Fatemeh Almodaresi, Prashant Kumar Pandey, R. Patro

Publication date 27 May 2020

Full work available at URL https://drops.dagstuhl.de/opus/volltexte/2017/7657/pdf/LIPIcs-WABI-2017-18.pdf/

zbMATH Keywords

succinct data structuresde Bruijn graphcolored de Bruijn graphrank and select operation

Mathematics Subject Classification ID

Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Recommendations

• Recoloring the colored de Bruijn graph
• Succinct de Bruijn graphs
• Bidirectional variable-order de Bruijn graphs
• Bidirectional Variable-Order de Bruijn Graphs
• Indexing variation graphs

Cites work

• Bloom filter trie -- a data structure for pan-genome storage
• Efficient Storage and Retrieval by Content and Address of Static Files
• Succinct Indexable Dictionaries with Applications to Encoding $k$-ary Trees, Prefix Sums and Multisets
• Succinct de Bruijn graphs

Cited in

(7)

• Space efficient merging of de Bruijn graphs and Wheeler graphs
• Recoloring the colored de Bruijn graph
• Comparative genomics with succinct colored de Bruijn graphs
• Compression algorithm for colored de Bruijn graphs
• An index for sequencing reads based on the colored de Bruijn graph
• Space-efficient merging of succinct de Bruijn graphs
• Rainbowfish

Describes a project that uses

Uses Software

• KMC
• SDSL
• GATB
• VARI
• GitHub

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