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thesistopics [2025/03/21 13:42]
leonard [SAT solving solutions for rearrangement problems (Bachelor/Master)] 		thesistopics [2025/03/31 17:32] (current)
arempel [<TITLE> (Bachelor/Master)]
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 While Integer Linear Programming (ILP) is commonly used to address this challenge, it has been recently observed that SAT formulations of the same problems may offer a faster alternative. The project involves converting an existing ILP solution for genomic rearrangement quantification into a SAT-based solution, leveraging SAT solvers'​ computational efficiency. While Integer Linear Programming (ILP) is commonly used to address this challenge, it has been recently observed that SAT formulations of the same problems may offer a faster alternative. The project involves converting an existing ILP solution for genomic rearrangement quantification into a SAT-based solution, leveraging SAT solvers'​ computational efficiency.
  
-===== <​TITLE> ​(Bachelor/​Master) ===== +Contact [[https://​ekvv.uni-bielefeld.de/​pers_publ/​publ/​PersonDetail.jsp?​personId=129443261 |Leonard]] for details. 
-<Project description>​ +===== Plasmid recovery/​assembly from long reads (Bachelor/​Master) ===== 
 +Despite advances in long-read sequencing technologies,​ plasmid assembly remains a significant challenge. Current state-of-the-art assemblers often fail to recover plasmids, especially those smaller than 10‎kb. This limitation is concerning because small plasmids often harbor important virulence and antimicrobial resistance genes. Popular assemblers such as Flye, Miniasm, Raven, and Canu show variable success, with recovery rates dropping dramatically for smaller plasmids. Furthermore,​ when plasmids are recovered, they often appear as multiple copies or are misassembled into the chromosome, highlighting fundamental limitations of current assembly algorithms. We are developing a novel pangenomic approach that uses gene identification within long reads and //k//-mers over the gene alphabet to improve the quality of the assembly graph. The main tasks for the students will be to analyze the performance of this method and to potentially improve it. ‎ Contact [[https://​ekvv.uni-bielefeld.de/​pers_publ/​publ/​PersonDetail.jsp?​personId=108064501|Andreas]] for details.
 ===== <​TITLE>​ (Bachelor/​Master) ===== ===== <​TITLE>​ (Bachelor/​Master) =====
 <Project description>​ <Project description>​