Resources

Training Resources

1. Broad Institute’s Training Resources

1.1 Viral Genomics Workshops

These workshops provide hands-on training in genomic analysis workflows, focusing on the study of viral genomes using next-generation sequencing (NGS) data. Hosted by the Broad Institute, they offer practical insights into cutting-edge tools and techniques for viral surveillance, assembly, and data interpretation.

Course Link: Viral Genomics Workshops

1.2 Viral De Novo Assembly Workflows on the Terra Cloud Platform

This course focuses on viral de novo assembly workflows using Illumina sequencing data. It specifically uses Lassa virus data as a case study and leverages the Terra cloud platform to demonstrate the assembly process.

Course Link: Viral De Novo Assembly Workflows on Terra Cloud Platform

1.3 Terra Training Archive: Access Previous Workshops & Event Materials

The Terra Support platform offers a comprehensive repository of materials from previous training events, designed to assist users in effectively utilizing Terra's data science infrastructure. These resources encompass a wide range of topics, including cloud-native pipeline development, data repository management, and machine learning applications.

Key Highlights

🔹 Cloud-Native Pipelines:  
   Workshops such as the July 2024 session focused on creating & running cloud-native
   pipelines using WDL, Dockstore & Terra.

🔹 Data Repository Management:  
   The March and February 2024 workshops introduced users to the Terra Data Repository
   (TDR), covering essential features like data organization, secure collaboration, &
   efficient data retrieval methods.

🔹 Machine Learning Integration:
   In September 2023, a collaborative workshop with Google's AI in Healthcare and Life
   Sciences team showcased the integration of Vertex AI on Terra.

🔹 Interactive Analysis Tools:
   Regular sessions, including those in October 2023, provided introductions to Terra's
   interactive analysis capabilities, emphasizing the use of Jupyter Notebooks
   for data exploration & visualization.

🔹 Specialized Applications:
   Workshops have also delved into niche areas such as structural variant discovery using
   the GATK-SV pipeline (February 2023) & the integration of DRAGEN-GATK workflows
   (October 2022), catering to advanced genomic analysis needs.

Each event's materials typically include presentation slides, video recordings, and tutorial workspaces, enabling users to revisit and practice the concepts discussed. These resources are invaluable for both new and experienced users aiming to enhance their proficiency with Terra's platform.

Events Link: Previous Event Materials on Terra Cloud Platform

Theiagen Genomics

Theiagen Genomics is a leading bioinformatics company specializing in infectious disease genomics, pathogen surveillance, and public health data analysis. They provide cutting-edge solutions for next-generation sequencing (NGS) data interpretation, enabling researchers and public health institutions to track and respond to emerging threats. With a strong focus on capacity building and open-source bioinformatics tools, Theiagen Genomics empowers global health communities to harness genomic data for better disease control and prevention.

TheiaProk:
Workflow Series

Theiagen Public Health Bioinformatics Resources:
PHB v1.2.1 Resources

Theiagen Public Health Bioinformatics Resources:
Theiagen’s Public Health Bioinformatics

Theiagen Public Health Bioinformatics Resources:
Theiagen’s Public Health Bioinformatics relationships between the workflows

Theiagen Public Health Bioinformatics Resources (Docker page):
Docker Collection