Presentations

Below, you'll find a curated collection of talks, posters, and blog posts that delve into various aspects of Bactopia. These resources offer valuable insights into Bactopia's capabilities, features, and community contributions. If you have questions about any of the presentations or wish to utilize the material for your own research or educational purposes, please don't hesitate to contact me. I'm more than happy to assist and discuss further.

Workshops

• Workshop for using Bactopia (March 2023)
  A workshop conducted with the CDC Enteric Diseases Laboratory Branch (EDLB), introducing Bactopia and Bactopia Tools. This workshop provided a background on the many moving parts of Bactopia. Participants analyzed genomes with Bactopia and used the Bactopia Tools to seamlessly expand their analyses. For this workshop we followed the steps provided by Bactopia Workshop.
  Slides: PDF

Talks

• Bactopia - Enhancing and expanding the Bactopia framework (October 2024)
  A brief talk presented by Dr. Robert A Petit III at ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (ASMNGS). This talk highlighted how Bactopia has evolved from an end-to-end pipeline to more of a framework to rapidly adapt to user needs.
  Slides: PDF

• Introduction to Bactopia for Bacterial Genome Analysis (June 2024)
  A talk presented by Dr. Robert A Petit III at the monthly Technical Outreach and Assistance for States Teams (TOAST). This talk introduced participants to Bactopia and how they can make use of it in their genomic analyses.
  Slides: PDF

• Bactopia v3 - Enhancements for public health genomic surveillance (December 2023)
  A brief talk presented by Dr. Robert A Petit III at the Nextflow Summit - Boston 2023. This talk highlighted how Bactopia was rebuilt in version 3 to better support on-going genomic surveillance of bacterial pathogens.
  Slides: PDF

• Designing mechanisms into Bactopia to support its users and contribute back to the community (October 2022)
  A brief talk presented by Dr. Robert A Petit III at the Nextflow Summit 2022. This is a brief talk on how Bactopia was designed to reduce the maintenance burden while contributing back to the community.
  Video: YouTube
  Slides: PDF

• Bactopia & it's usage of nf-core components (July 2022)
  A brief talk presented by Dr. Robert A Petit III at the nf-core Bytesize sries. This is a brief talk on how Bactopia has modified and applied some nf-core components.
  Video: YouTube
  Slides: PDF

• Using Bactopia for the complete analysis of bacterial genomes (April 2022)
  A brief talk presented by Dr. Robert A Petit III at the African Bioinformatics Netwrok Webinar. In this talk background on Bactopia is provided and a demonstration how you can use it in your own analyses.
  Video: YouTube
  Slides: Web, PDF

• Deeper dives, workflows and Bactopia (February 2022)
  A brief talk presented by Dr. Robert A Petit III at the CLIMB Big Data - Bioinformatics Skills for Microbial Genomics Workshop, covering some topics including Bioconda, nf-core, and a slight peek behind the scenes of Bactopia.
  Video: YouTube
  Slides: Web, PDF

• Bactopia and using workflow managers in bioinformatics (January 2022)
  In episodes 72 and 73 of the Micro Binfie Podcast we discussed the origins of Bactopia and all the fun things Bactopia does. We also discuss why you should consider using workflow managers in you bioinformatic analyses.
  Sound Cloud: Part 1, Part 2

• Integrating Staphopia into S. aureus genomic investigations (February 2021)
  A brief talk presented by Dr. Robert A Petit III at the Virtual S. aureus Seminar Series Early Career Symposium, demonstrating how you can use Staphopia for the analysis of S. aureus. Staphopia is now a part of Bactopia.
  Video: YouTube
  Slides: Web, PDF

• Bacterial Genome Analysis Using Bactopia (May 2020)
  The talk presented by Dr. Robert A Petit III at State Public Health Bioinformatics (StaPH-B) Monthly Webinar which provides a introduction into Bactopia and some of the earlier practices implemented into Bactopia.
  Video: YouTube
  Slides: Web, PDF

• Bacterial Genome Analysis Workflows: Staphopia and Bactopia (March 2020)
  The talk presented by Dr. Timothy Read at NIAID Webinar Series which provides an overview of the Bactopia and Staphopia pipelines and how you can use them to investigate bacterial genomes.
  Slides: Web, PDF

Posters

• Expanding Bactopia as a framework for bacterial, fungal, and metagenomic analysis (September 2024)
  A poster presented by Dr. Robert A Petit III at the AMD Days 2024 conference outlining the latest changes in Bactopia, including new named workflows and AllTheBacteria support.
  Slides: PDF

• Expanding Bactopia as a framework for bacterial, fungal, and metagenomic analysis (May 2024)
  A poster presented by Dr. Robert A Petit III at the Sequencing to Function: Analysis and Applications for the Future conference outlining the latest changes in Bactopia, including new named workflows and AllTheBacteria support.
  Slides: PDF

• Expanding Bactopia as a framework for bacterial, fungal, and metagenomic analysis (May 2024)
  A poster presented by Dr. Robert A Petit III at the APHL 2024 conference outlining the latest changes in Bactopia, including new named workflows and AllTheBacteria support.
  Slides: PDF

• Bactopia v3 - Enhancements for on-going genomic surveillance of bacterial pathogens (June 2023)
  A poster presented by Dr. Robert A Petit III at the Sequencing to Function: Analysis and Applications for the Future conference highlighting the latest changes in Bactopia v3.
  Slides: PDF

• Supporting the bioinformatics community by supporting Bactopia users (October 2022)
  A poster presented by Dr. Robert A Petit III at the ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (ASMNGS) conference outlining how Bactopia was designed to reduce the maintenance burden while contributing back to the community.
  Slides: PDF

• Using Bactopia for highly scalable, portable and customizable bacterial genome analyses (August 2022)
  A poster presented by Dr. Robert A Petit III at the 11^th International Conference on Emerging Infectious Diseases (ICEID) outlining how you can use Bactopia in your bacterial genome analyses.
  Slides: PDF

• Using Bactopia for highly scalable, portable and customizable bacterial genome analyses (May 2022)
  A poster presented by Dr. Robert A Petit III at Sequencing to Function: Analysis and Applications for the Future in-person conference outlining how you can use Bactopia in your bacterial genome analyses.
  Slides: Web, PDF

• Bactopia v2: Highly scalable, portable and customizable bacterial genome analyses (April 2022)
  A poster presented by Dr. Robert A Petit III at APHL Annual Conference covering Bactopia and ways to use it in your own analyses.
  Video: YouTube
  Slides: Web, PDF

• Bactopia v2: Highly scalable, portable and customizable bacterial genome analyses (April 2022)
  A poster presented by Dr. Robert A Petit III at Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (Virtual Conference) covering Bactopia and ways to use it in your own analyses.
  Video: YouTube
  Slides: Web, PDF

• Bactopia v2: Highly scalable, portable and customizable bacterial genome analyses (March 2022)
  A poster presented by Dr. Robert A Petit III at Sequencing to Function: Analysis and Applications for the Future previewing version 2 of Bactopia and the many changes it will bring.
  Slides: Web, PDF

• Bactopia v2: Highly scalable, portable and customizable bacterial genome analyses (September 2021)
  A poster presented by Dr. Robert A Petit III at Sequencing to Function: Analysis and Applications for the Future previewing version 2 of Bactopia and the many changes it will bring.
  Video: YouTube
  Slides: Web, PDF

• Using Bactopia to process 67,000 Staphylococcus aureus genomes with AWS Batch (May 2021)
  A poster presented by Dr. Robert A Petit III at Applied Bioinformatics & Public Health Microbiology 2021 which outlines how Bactopia was used to process 67,000 genomes in just 5 days (!) using AWS Batch.
  Video: YouTube
  Slides: Web, PDF

• A Flexible Pipeline for Complete Analysis of Bacterial Genomes (December 2020)
  A poster presented by Dr. Robert A Petit III at the 4^th ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (ASMNGS) which provides an overview of Bactopia, Bactopia Datasets, and Bactopia Tools.
  Slides: Web, PDF

Blog Posts

• An introduction to running Bactopia on Amazon Web Services (May 2021)
  A blog post written by Dr. Timothy Read, outlining from start to finish how he set up Bactopia to run on Amazon Web Services (AWS).

• Using AWS Batch to process 67,000 genomes with Bactopia (December 2020)
  A blog post written by Dr. Robert A Petit III, providing an in-depth look into how he used Bactopia to process 67k genomes on AWS Batch.