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UID:50@cds.iisc.ac.in
DTSTART;TZID=Asia/Kolkata:20240415T090000
DTEND;TZID=Asia/Kolkata:20240415T100000
DTSTAMP:20240412T113508Z
URL:https://cds.iisc.ac.in/events/m-tech-research-thesis-colloquium-cds-se
 quence-alignment-to-cyclic-pangenome-graphs/
SUMMARY:M.Tech Research Thesis {Colloquium}: CDS: "Sequence Alignment to Cy
 clic Pangenome Graphs"
DESCRIPTION:DEPARTMENT OF COMPUTATIONAL AND DATA SCIENCES\nM.Tech Research 
 Thesis Colloquium\n\n\n\nSpeaker : Ms. Jyotshna Rajput\n\nS.R. Number : 06
 -18-01-10-22-21-1-19943\n\nTitle :"Sequence Alignment to Cyclic Pangenome 
 Graphs"\nResearch Supervisor: Dr. Chirag Jain\nDate &amp\; Time : April 15
 \, 2024 (Monday) at 09:00 AM\n\nVenue : The Thesis Colloquium will be held
  on MICROSOFT TEAMS\n\n&nbsp\;\n\n\n\nABSTRACT\n\nThe growing availability
  of genome sequences of several species\, including humans\, has created t
 he opportunity to utilize multiple reference genomes for bioinformatics an
 alyses and improve the accuracy of genome resequencing workflows. Graph-ba
 sed data structures are suitable for compactly representing multiple close
 ly related reference genomes. Pangenome graphs use a directed graph format
 \, where vertices are labeled with strings\, and the individual reference 
 genomes are represented as paths in the graph. Aligning sequences (reads) 
 to pangenome graphs is fundamental for pangenome-based genome resequencing
 . The sequence-to-graph alignment problem seeks a walk in the graph that s
 pells a sequence with minimum edit distance from the input sequence. Howev
 er\, exact algorithms for solving this problem are unlikely to scale due t
 o the known hardness of this problem. Co-linear chaining is a well-studied
  and commonly used heuristic alternative for quickly aligning reads to a g
 raph. However\, the known chaining algorithms are restricted to directed a
 cyclic graphs (DAGs) and are not trivially generalizable to cyclic graphs.
  This limitation must be addressed because pangenome graphs often contain 
 cycles due to inversions\, duplications\, or copy number mutations within 
 the reference genomes.\n\nThis thesis presents the first practical formula
 tion and algorithm for co-linear chaining on cyclic pangenome graphs. Our 
 algorithm builds upon the known chaining algorithms for DAGs. We propose a
  novel iterative algorithm to handle cycles and provide rigorous proof of 
 correctness and runtime complexity. Our algorithm also exploits the domain
 -specific small-width property of pangenome graphs. The proposed optimizat
 ions enable our algorithm to scale to large human pangenome graphs. We imp
 lemented our algorithm in C++ and referred to it as PanAligner (https://gi
 thub.com/at-cg/PanAligner). PanAligner is an end-to-end long-read aligner 
 for pangenome graphs. We evaluated its speed and accuracy by aligning simu
 lated long reads to a cyclic human pangenome graph comprising 95 haplotype
 s. We achieved superior read mapping accuracy using PanAligner compared to
  existing methods.\n\n\n\nALL ARE WELCOME
CATEGORIES:MTech Research Thesis Colloquium
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