October 2022 - MPXV_ampliconseq

Several guests (Chantal Vogels, Nick Chen, Kevin Libuit, Erin Young) were invited to give updates on amplicon sequencing protocols for monkeypox virus (MPXV), and bioinformatic analysis methods for consensus sequence generation of MPXV.

June 2022 - BugSeq

This StaPH-B call focuses on BugSeq, an automated, scalable DNA sequencing analysis platform for clinical and public health labs created by Sam Chorlton and Josh Chorlton.

June 2022 - Right-sizing

This call focuses on work performed to find the appropriate sampling sizes for variant surveillance in SARS-CoV-2 specifically, and tools created to determine the right number of sequences for different purposes, presented by Shirlee Wohl, PhD.

April 2022 - NCBI-Bioprojects

This call focuses on NCBI Bioprojects at the request of StaPH-B users, with guest speakers Karen Clark, PhD and Nuala A. O’Leary presenting.

February 2022 - Freyja

This month’s StaPH-B call welcomed Josh Levy, PhD of the Scripps Research Institute to speak about the background and usage of the software Freyja, a tool for estimating the true lineage abundances of SARS-CoV-2 in a sample. Slides

December 2021 - NBS

For this month’s StaPH-B call, three newborn-screening (NBS) bioinformaticians, Gretchen Cote in Virginia, Sam Marcellus in Texas, and Jessica Respress in New York, speak about their roles and responsibilities, and the different approaches states have taken to NBS bioinformatics.

November 2021 - UShER

In this call, Angie Hinrichs (UCSC), Jade Wang (NYC Public Health) and Michelle Su (NYC Public Health) explained how pango’s UShER setting works, how it’s different from the default pangoLEARN, as well as reported on some findings from NYC Delta-wave data. Slides

October 2021 - CLIMB-COVID

StaPH-B hosted its second ever international call, with guest Sam Nicholls from the UK’s CLIMB-COVID initiative which pulls together an impressive amount of SARS-CoV-2 sequencing data from across the UK into a central place for analysis, rapid turnaround, and epidemiological application. Sam introduced the platform, the structure, and some challenges and hurdles that had to be overcome during its implementation.

September 2021 - Closing (Some of the issues with circular) Genomes

In this call, Erin Young from UTPHL gave an overview of the Trycycler tool for consensus of long read assemblies and closing circular genomes. Differences between long and short read sequencing was discussed, as well as some pitfalls and issues that can arise when closing circular genomes. Slides

July 2021 - Wastewater Surveillance for SARS-CoV-2

In this webinar, guest speakers from Virginia’s department of Health (VDH) and the CDC’s National Wastewater Surveillance System (NWSS) gave overviews of wastewater surveillance and sequencing for SARS-CoV-2 at the state and federal levels.

June 2021 - NCBI's Viral Annotation DefineR (VADR)

In this webinar, guest speaker Eric Nawrocki gave an overview of VADR, the viral annotation tool which is used to flag SARS-CoV-2 and other viral genome assemblies submitted to NCBI for potential issues. Changes and updates to the tool to provide more accurate annotations were discussed.

February 2021 - CLIA Validation of Next Generation Sequencers

In this webinar, a guest panel of speakers (Nicolas Matluck, Maryann Turnsek, Kelly Oakeson, Rituparna Mukhopadhyay, and Matthew Sylvester) discussed experiences with CLIA validating and compliance of next generation sequencing. Questions and answers about the different approaches taken by the different groups followed.

December 2020 - Special Episode COVID-19 on B.1.1.7

In this webinar, StaPH-B members and SPHERES members assembled together, had a comprehensive overview of the recent B.1.1.7 SARS-CoV-2 variant, specimen testing details of the first Colorado case, and discussed how the US can enhance our molecular surveillance for the B.1.1.7 variant and possible future COVID-19 variant strains.

November 2020 - NCBI Virus

In this webinar, Dr. Eneida Hatcher of NCBI presented on the utility and some exciting new features of NCBI Virus, a resource for viral sequence analysis and visualization of SARS-CoV-2 genome data submitted to NCBI.

October 2020 - ViPR and PATRIC

In this webinar, Richard Scheuermann at JCVI presents on the resources virus pathogen database and analysis resource (ViPR) and pathosystems resource integration center (PATRIC). A breif overview of both of the systems, their functionality and uses was given.

August 2020 - Candida auris WGS

This webinar featured Nancy Chow and Rory Welsh of the CDC mycotic diseases branch. They spoke about the growing threat of the drug resistant organism Candida auris, and some whole genome sequencing initiatives that are underway to detect and prevent the spread of this particular pathogen.

July 2020 - Special Episode COVID-19 on pangolin, llama, civet

This call welcomed Aine O’Toole from the Rambaut lab at the Univeristy of Edinburgh in the UK. She discussed a few different tools she and others have been working on, pangolin, llama, and civet, all aimed at lineage typing the SARS-CoV-2 virus circulating around the UK and abroad. She discussed development, plans going forward, as well as the role they play in the COG-UK consortium.

June 2020 - Special Episode COVID-19 on MicrobeTrace

In this StaPH-B webinar, we invited Ellsworth Campbell to discuss MicrobeTrace, a “web-based tool to visually render networks from surveillance, epi investigations, and genetic analysis” that can be leveraged to support COVID-19 outbreak investigations. Ellsworth presented on the MicrobeTrace platform and provided useful information on how epidemiologists can utilize MicrobeTrace reports and visualizations to inform public health action. Following this, the floor was opened for a Q&A session.

May 2020 - Special Episode COVID-19 on Tailed Amplicon Method for Sequencing SARS-CoV-2

In this webinar, Dr. Daryl Gohl from the University of Minnesota discusses his work on: A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2.

May 2020 - Special Episode COVID-19 on EDGE

In this webinar, we continued our discussion regarding SARS-CoV-2 (SC2) genome analysis: Patrick Chain and his team (LANL) discussed a containerized workflow based on the EDGE platform for SC2 sequence data QC, genome assembly, and SNP analysis.

May 2020 - Bactopia

In this webinar, Robert Petit and Tim Read from Emory University present on Bactopia, “an extensive workflow for processing Illumina sequencing of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!” Bactopia, built on the Nextflow platform, was designed to provide efficient comparative genomic analysis for any bacterial species or genus. Bactopia can be accessed through GitHub, Docker, Singularity, and Conda.

April 2020 - Special Episode COVID-19 on Nextstrain local builds

In this webinar, Heather Blankenship–a bioinformatics scientist at the Michigan public health laboratory–spoke about her experience setting up a local NextStrain build for real-time COVID-19 surveillance in Michigan. Heather discussed the advantages of local NextStrain builds for state laboratories and outlined the steps she has taken to set things up in her environment. Following this, we opened the floor for a Q&A session with Heather. Slides

April 2020 - Special Episode COVID-19 on Nextstrain

In this webinar, Alli Black, a PhD candidate in the Bedford Laboratory who has been working extensively on the NextStrain platform, spoke with StaPH-B. During this call, Alli provided a brief introduction to NextStrain, a valuable resource for genomic data analysis and visualization, and demoed some of NextStrain’s functionality. Following this, we opened the floor for a Q&A session with Alli. Slides

March 2020 - Special Episode COVID-19 on SARS-CoV-2 Sequencing

In response to the COVID-19 pandemic, we utilized our scheduled call to host a discussion regarding the various COVID-19 sequencing and analysis protocols available to the public health laboratories. A specific focus on the ARTIC Network’s protocols for COVID-19 sequencing and genome assembly, as these seem the most appropriate for US state laboratories. Slides

February 2020 - Compute Workflow Management

In this webinar, Danny Park, group lead of the viral computational genomics at the Broad Institute and technical consultant for the North East Bioinformatics Regional Resource, spoke about scientific compute workflow management. He provided an overview of WDL and Cromwell and how the Broad Institute and many other genomics institutions are taking advantage of these systems to improve scalability (cloud, cluster, single machine), portability between institutions, and reproducibility.

January 2020 - StaPH-B Toolkit

Kelsey Florek and Kevin Libuit presented on the StaPH-B ToolKit. The StaPH-B ToolKit is a Python library written to relieve the burden of major bioinformatics challenges Kelsey and Kevin have identified throughout our respective regions: access to and proper use of StaPH-B docker images, capture of data lineage information, configurable and distributable pipeline parameters, and the portability of StaPH-B developed workflows.

January 2020 - StaPH-B Toolkit

In this webinar, Kelsey Florek and Kevin Libuit presented on the StaPH-B ToolKit. The StaPH-B ToolKit is a Python library written to relieve the burden of major bioinformatics challenges Kelsey and Kevin have identified throughout their respective regions: access to and proper use of StaPH-B docker images, capture of data lineage information, configurable and distributable pipeline parameters, and the portability of StaPH-B developed workflows.

December 2019 - Madrone by Chan-Zuckerberg BioHub

Lucy Li and David Dynerman from the Chan-Zuckerberg BioHub to speak about Madrone, a user-friendly bioinformatics platform for cluster analysis and AMR gene detection for carbapenem-resistant Enterobacteriaceae isolates. Madrone was developed in collaboration between the Chan-Zuckerberg BioHub and the Alameda County (CA) Public Health Laboratory to address Alameda’s bioinformatics needs.

November 2019 - NGS Validations

We invited Nick Matluk, the Microbiology and CLIA Technical Supervisor at the Maine state laboratory. Nick provided background on Maine’s use of WGS to support infectious disease investigations and detailed their approach to CLIA validation of bioinformatics workflows on Qiagen’s CLC Genomics Workbench platform.

October 2019 - Singularity Container System

For this month’s call, we had a second discussion on container platforms: Jake Garfin (Minnesota Department of Health) and Curtis Kapsak (Centers for Disease Control and Prevention) presented an overview of the Singularity container system, it’s similarities and differences compared to Docker, and a short usage demonstration. This is particularly helpful for laboratories that are interested in using the StaPH-B Docker Images, but lack root privileges required to run Docker in their compute environments.

July 2019 - Scott Becker, Executive Director of APHL

Scott Becker, Executive Director of APHL spoke about the field of bioinformatics, its current impact on public health, and where things may be going in the years to come. Scott also offered his advice on keeping a workgroup like StaPH-B a cohesive and effective resource for public health.

May 2019 - Genetic Determinants of AMR

In this webinar, Jessica Chen from the CDC’s National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) to discuss her laboratory’s strategy to developing a robust bioinformatics pipeline for rapid detection of AMR determinants from WGS data.