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UID:34@cds.iisc.ac.in
DTSTART;TZID=Asia/Kolkata:20240131T140000
DTEND;TZID=Asia/Kolkata:20240131T150000
DTSTAMP:20240126T064354Z
URL:https://cds.iisc.ac.in/events/m-tech-research-thesis-colloquium-cds-sc
 alable-read-alignment-algorithm-for-cyclic-pangenome-graphs/
SUMMARY:M.Tech Research Thesis {Colloquium}: CDS : "Scalable read alignment
  algorithm for cyclic 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 :"Scalable read alignment algorithm for c
 yclic pangenome graphs"\nResearch Supervisor: Dr. Chirag Jain\nDate &amp\;
  Time : January 31\, 2024 (Wednesday) at 02:00 PM\nVenue : # 102 CDS Semin
 ar Hall\n\n\n\nABSTRACT\n\nThe growing availability of genome sequences of
  several species\, including humans\, has created the opportunity to utili
 ze multiple reference genomes for bioinformatics analyses and improve the 
 accuracy of genome resequencing workflows. Graph-based data structures are
  suitable for compactly representing multiple closely related reference ge
 nomes. Pangenome graphs use a directed graph format\, where vertices are l
 abeled 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 spells a sequence with m
 inimum edit distance from the input sequence. However\, exact algorithms f
 or solving this problem are unlikely to scale due to the known hardness of
  this problem. Co-linear chaining is a well-studied and commonly used heur
 istic alternative for quickly aligning reads to a graph. However\, the kno
 wn chaining algorithms are restricted to directed acyclic graphs (DAGs) an
 d are not trivially generalizable to cyclic graphs. This limitation must b
 e addressed because pangenome graphs often contain cycles due to inversion
 s\, duplications\, or copy number mutations within the reference genomes.\
 n\nThis thesis presents the first practical formulation and algorithm for 
 co-linear chaining on cyclic pangenome graphs. Our algorithm builds upon t
 he known chaining algorithms for DAGs. We propose a novel iterative algori
 thm to handle cycles and provide rigorous proof of correctness and runtime
  complexity. Our algorithm also exploits the domain-specific small-width p
 roperty of pangenome graphs. The proposed optimizations enable our algorit
 hm to scale to large human pangenome graphs. We implemented our algorithm 
 in C++ and referred to it as PanAligner (https://github.com/at-cg/PanAlign
 er). PanAligner is an end-to-end long-read aligner for pangenome graphs. W
 e evaluated its speed and accuracy by aligning simulated long reads to a c
 yclic human pangenome graph comprising 95 haplotypes. We achieved superior
  read mapping accuracy using PanAligner compared to existing methods.\n\n\
 n\nALL ARE WELCOME
CATEGORIES:Ph.D. Thesis Colloquium
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