Rainbowfish: a succinct colored de Bruijn graph representation

DOI10.4230/LIPICS.WABI.2017.18MaRDI QIDQ5111820zbMATH OpenOpenAlexFDO

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

colored de Bruijn graphde Bruijn graphrank and select operationsuccinct data structures

Mathematics Subject Classification ID

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

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 de Bruijn graphs
• Succinct Indexable Dictionaries with Applications to Encoding k-ary Trees, Prefix Sums and Multisets

Cited in

(7)

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

Describes a project that uses

Uses Software

• SDSL
• KMC
• GATB
• VARI
• GitHub

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