The contig assembly problem and its algorithmic solutions

DOI10.1007/978-3-319-59826-0_12MaRDI QIDQ3305536zbMATH OpenOpenAlexFDO

Authors 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)

Recommendations

• Combinatorial algorithms for DNA sequence assembly
• DNA sequence assembly involving an acyclic graph model
• scientific article; zbMATH DE number 956614
• scientific article; zbMATH DE number 826053
• scientific article; zbMATH DE number 1445328

Cites work

• scientific article; zbMATH DE number 432779 (Why is no real title available?)
• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• An Eulerian path approach to DNA fragment assembly
• Combinatorial algorithms for DNA sequence assembly
• Scaling metagenome sequence assembly with probabilistic de Bruijn graphs
• Space/time trade-offs in hash coding with allowable errors
• The consensus string problem for a metric is NP-complete

Cited in

(14)

• scientific article; zbMATH DE number 826053 (Why is no real title available?)
• The matrix iteration algorithm solving an enumeration problem on bacterial complete genomes
• Safe and complete contig assembly via omnitigs
• Probabilistic modeling and analysis of DNA fragmentation
• Seeding strategies and recombination operators for solving the DNA fragment assembly problem
• Optimal Omnitig Listing for Safe and Complete Contig Assembly
• Rearrangement of DNA fragments: a branch-and-cut algorithm.
• DNA sequence assembly involving an acyclic graph model
• Modified classical graph algorithms for the DNA fragment assembly problem
• Linear-time superbubble identification algorithm for genome assembly
• The sequence reconstruction problem
• An integer programming approach to DNA sequence assembly
• A study of computational genome assembly by graph theory
• Fuzzy genome sequence assembly for single and environmental genomes

Describes a project that uses

Uses Software

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

This page was built for publication: The contig assembly problem and its algorithmic solutions

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q3305536)