Linking indexing data structures to de Bruijn graphs: construction and update

DOI10.1016/j.jcss.2016.06.008zbMath1423.68121OpenAlexW2484870067MaRDI QIDQ2424683

Thierry Lecroq, Eric Rivals, Bastien Cazaux

Publication date: 25 June 2019

Published in: Journal of Computer and System Sciences (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcss.2016.06.008

zbMATH Keywords

overlapalgorithmsindexbioinformaticssuffix arraysuffix treeassemblydata structuredynamic updatecontracted de Bruijn graph

Mathematics Subject Classification ID

Analysis of algorithms (68W40) Protein sequences, DNA sequences (92D20) Data structures (68P05)

Related Items

Reverse-Safe Text Indexing ⋮ Special issue: Selected papers of the 9th international conference on language and automata theory and applications, LATA 2015

Uses Software

• SPAdes
• MindTheGap
• LoRDEC
• IDBA

Cites Work

• Truncated suffix trees and their application to data compression.
• On-line construction of suffix trees
• Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree
• Suffix Arrays: A New Method for On-Line String Searches
• A Space-Economical Suffix Tree Construction Algorithm
• Algorithms on Strings, Trees and Sequences
• An Eulerian path approach to DNA fragment assembly
• Succinct de Bruijn Graphs
• From Indexing Data Structures to de Bruijn Graphs
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