AStarix: Fast and Optimal Sequence-to-Graph Alignment

DOI10.1007/978-3-030-45257-5_7zbMath1500.92076OpenAlexW3018787322MaRDI QIDQ5041800

André Kahles, Harun Mustafa, Martin Vechev, Pesho Ivanov, Benjamin Bichsel, Gunnar Rätsch

Publication date: 14 October 2022

Published in: Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-3-030-45257-5_7

zbMATH Keywords

shortest pathnext-generation sequencingoptimal alignmentgenome graph\(\mathrm{A}^\star\) algorithm

Mathematics Subject Classification ID

Applications of graph theory (05C90) Protein sequences, DNA sequences (92D20)

Related Items

AStarix ⋮ Fast and optimal sequence-to-graph alignment guided by seeds

Uses Software

• Bowtie 2
• deBGA
• BWA
• LoRDEC
• Mason
• hybridSPAdes
• BrownieAligner
• ART

Cites Work

• Comparison of biosequences
• Lazy dynamic-programming can be eager
• An algorithm for the distance between two finite sequences
• On the complexity of sequence to graph alignment
• Generalized best-first search strategies and the optimality of A*
• Indexing Variation Graphs