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klimke edited this page Nov 23, 2020 · 4 revisions

ASM NGS NCBI Pre-Conference Workshop

Introduction to NCBI Pathogen Detection and Google Cloud Based Resources for Pathogen NGS Analysis

Announcement

Workshop organization

  • Pre-workshop prep to get accounts and setup ready for the workshop

  • Slides

  • SlidesPart1 -- Intro to Cloud

  • SlidesPart2 -- NCBI in the Cloud

  • SlidesPart3 -- Other tools

  • SlidesPart4 -- NCBI Pathogen Detection

  • SlidesPart5 -- Background to analysis

  • Setup -- Getting started with GCP, creating your VM and bucket All three parts of the analysis during the workshop are from this paper: Chng, Li, and Bertrand et al., 2020

  • Project 1 -- examine resistome of Acinetobacter baumannii set with NCBI AMRFinderPlus tool

  • Project 2 -- examine relationship of Acinetobacter baumannii s6 cluster with independently studied Kuwaiti Ab isolates

  • Project 3 -- extract reads from metagenomes using plasmid references, examine relationship of plasmids derived from this step

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