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UID:58@cds.iisc.ac.in
DTSTART;TZID=Asia/Kolkata:20240708T113000
DTEND;TZID=Asia/Kolkata:20240708T123000
DTSTAMP:20240619T064050Z
URL:https://cds.iisc.ac.in/events/m-tech-research-thesis-defense-cds-08-ju
 ly-2024-sequence-alignment-to-cyclic-pangenome-graphs/
SUMMARY:M.Tech Research: Thesis Defense: CDS: 08\, July 2024 "Sequence Alig
 nment to Cyclic Pangenome Graphs"
DESCRIPTION:DEPARTMENT OF COMPUTATIONAL AND DATA SCIENCES\n\n\nM.Tech Resea
 rch Thesis Defense\n\n\n\n\nSpeaker                  : Ms. Jyotsh
 na Rajput\nS.R. Number         : 06-18-01-10-22-21-1-19943\nTitle  
                          : "Sequence Alignment to Cyclic Pang
 enome Graphs"\nThesis examiner :  Prof. L Sunil Chandran\, Dept. of Comp
 uter Science and Automation\, IISc.\nResearch Supervisor:  Dr. Chirag Jai
 n\nDate &amp\; Time          : July 08\, 2024 (Monday) at 11:30 AM\nV
 enue                       : CDS  # 308\n\n\n\n\n\nABSTRACT\n\
 n\nThe growing availability of genome sequences of several species\, inclu
 ding humans\, has created the opportunity to utilize multiple reference ge
 nomes for bioinformatics analyses and improve the accuracy of genome reseq
 uencing workflows. Graph-based data structures are suitable for compactly 
 representing multiple closely related reference genomes. Pangenome graphs 
 use a directed graph format\, where vertices are labelled with strings\, a
 nd the individual reference genomes are represented as paths in the graph.
  Aligning sequences (reads) to pangenome graphs is fundamental for pangeno
 me-based genome resequencing.\n\nThe sequence-to-graph alignment problem s
 eeks a walk in the graph that spells a sequence with minimum edit distance
  from the input sequence. Unfortunately the exact algorithms known for sol
 ving this problem are not scalable. Among the known heuristics\, co-linear
  chaining is a common technique for quickly aligning reads to a graph. How
 ever\, the known chaining algorithms are restricted to directed acyclic gr
 aphs (DAGs) and are not trivially generalizable to cyclic graphs. Addressi
 ng this limitation is important because pangenome graphs often contain cyc
 les due to inversions\, duplications\, or copy number mutations within the
  reference genomes.\n\nThis thesis presents the first practical formulatio
 n and algorithm for co-linear chaining on cyclic pangenome graphs. Our wor
 k builds upon the known chaining algorithms for DAGs. We propose a novel i
 terative algorithm to handle cycles and provide a rigorous proof of correc
 tness and runtime complexity. We also use the domain-specific small-width 
 property of pangenome graphs. The proposed optimizations enable our algori
 thm to scale to large human pangenome graphs. We implemented the algorithm
  in C++ and referred to it as PanAligner (https://github.com/at-cg/PanAlig
 ner). PanAligner is an end-to-end long-read aligner for pangenome graphs. 
 We evaluated its speed and accuracy by aligning simulated long reads to a 
 cyclic human pangenome graph comprising 95 haplotypes. We achieved superio
 r read mapping accuracy compared to existing methods.\n\n\n\n\n\n\nALL ARE
  WELCOME\n\n
CATEGORIES:Events,Thesis Defense
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