log in  |  register  |  feedback?  |  help  |  web accessibility
Logo
Outbreak cluster identification for food safety: algorithms in NCBI's Pathogen Detection Pipeline
Richa Agarwala - National Center for Biotechnology Information (NCBI)
Iribe Center, Room 4105 (Zoom link: https://umd.zoom.us/j/97287503999)
Thursday, February 23, 2023, 2:00-3:00 pm Calendar
  • You are subscribed to this talk through .
  • You are watching this talk through .
  • You are subscribed to this talk. (unsubscribe, watch)
  • You are watching this talk. (unwatch, subscribe)
  • You are not subscribed to this talk. (watch, subscribe)
Abstract

NCBI Pathogen Detection system integrates bacterial and fungal pathogen genomic sequences from numerous ongoing surveillance and research efforts whose sources include food, environmental sources such as water or production facilities, and patient samples. Foodborne, hospital-acquired, and other clinically infectious pathogens are included. One of the two major automated real-time analyses provided is a quick clustering of related pathogen genome sequences to identify potential transmission chains, helping public health scientists investigate disease outbreaks. In this talk, I will present the algorithms for the assembly (SKESA and SAUTE), clustering (Kmer and wgMLST), and SNP calling portion of the Pathogen Detection Pipeline.

Bio

Richa Agarwala is currently a senior scientist at NCBI. She leads a team that does research and development on methods for analyzing sequences. Some projects her team has contributed to are sequence assembly, BLAST, genome annotation, contamination screening, and Pathogen Detection Pipeline. Richa received her Ph.D. in Computer Science from Iowa State university in 1994, did a postdoctoral fellowship at the Center for Discrete Mathematics and Theoretical Computer Science in Rutgers University for "Special Year(s) in Mathematical Support for Molecular Biology" before coming to National Center for Human Genome Research at NIH (now NHGRI) in 1996. She joined NCBI in 1998.

This talk is organized by Erin Molloy