Rainbowfish: a succinct colored de Bruijn graph representation

DOI10.4230/LIPICS.WABI.2017.18zbMATH Open1436.92008OpenAlexW2950792513MaRDI QIDQ5111820FDOQ5111820

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/

Recommendations

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

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)

Cites Work

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

Cited In (7)

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

Uses Software

• KMC
• SDSL
• GATB
• VARI
• GitHub

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