The Contig Assembly Problem and Its Algorithmic Solutions

DOI10.1007/978-3-319-59826-0_12zbMath1457.68336OpenAlexW2754802449MaRDI QIDQ3305536

Géraldine Jean, Andreea Radulescu, Irena Rusu

Publication date: 7 August 2020

Published in: Algorithms for Next-Generation Sequencing Data (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-3-319-59826-0_12

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Algorithms on strings (68W32)

Uses Software

• ALLPATHS
• GAGE
• SSAKE
• SPAdes
• Velvet
• SOAPdenovo
• IDBA-UD
• ABySS
• QSRA
• SHARCGS
• PE-Assembler
• IDBA

Cites Work

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• The consensus string problem for a metric is NP-complete
• Combinatorial algorithms for DNA sequence assembly
• An Eulerian path approach to DNA fragment assembly
• Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
• Space/time trade-offs in hash coding with allowable errors

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