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--- thesistopics [2025/03/21 13:53]
leonard [SAT solutions for rearrangement problems (Bachelor/Master)]
+++ thesistopics [2025/03/31 17:32] (current)
arempel [<TITLE> (Bachelor/Master)]
@@ Line 13: / Line 13: @@
 Contact [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=129443261 |Leonard]] for details.
-===== <TITLE> (Bachelor/Master) =====
+===== Plasmid recovery/assembly from long reads (Bachelor/Master) =====
-<Project description>
+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) =====
 <Project description>

Genome Informatics

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