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
1.4 Explore detailed insights on the variant calling process and GATK best practices, accessible via a public Google Drive
Gain in-depth knowledge on the variant calling process and GATK best practices. Access comprehensive guides, workflows, and best practices through a publicly available Google Drive resource.
2. Taylor’s trainings
2.1 Taylor Paisie’s VEME 2024 NGS De Novo Assembly Tutorial
This course focuses on de novo genome assembly using next-generation sequencing (NGS) data, providing a comprehensive overview of workflows and practical exercises tailored for the VEME 2024 workshop. It includes step-by-step guidance on assembling viral genomes, with specific tools and methods to handle Illumina sequencing data efficiently.
Course Link: Taylor Paisie’s VEME 2024 NGS De Novo Assembly
2.2 Taylor Paisie’s VEME 2024 NGS Variant Calling
This course provides comprehensive guidance on variant calling workflows using next-generation sequencing (NGS) data. It is tailored for the VEME 2024 workshop and includes step-by-step instructions and examples.
Course Link: Taylor Paisie’s VEME 2024 NGS Variant Calling
3. A Beginner’s Guide to Genomic Data Analysis: Variant Calling
The link provides a beginner-friendly introduction to genomic data analysis, specifically focusing on variant calling, which involves identifying genetic variations in sequencing data.
It outlines the key steps in the process, including quality control, alignment of reads to a reference genome, and the use of tools like GATK for variant identification and filtering.
The guide emphasizes the importance of understanding the pipeline and highlights resources and tools to help newcomers get started with genomic data analysis.
Course Link:
A Beginner’s Guide to Genomic Data Analysis: Variant Calling
4. Selected Online Bioinformatics and Genomics Learning Platforms
Several online platforms offer bioinformatics and genomics courses, providing accessible and flexible learning opportunities for students, researchers, and professionals in the field.
FutureLearn provides a range of courses on genomics and bioinformatics, covering fundamental concepts, applications in healthcare, and emerging technologies. These courses are designed by leading institutions and cater to learners at different levels, from beginners to advanced practitioners.
Coursera offers extensive training in bioinformatics and genomics through courses developed by top universities and research organizations. The platform provides structured learning paths, including beginner-friendly introductions and specialized topics such as next-generation sequencing (NGS), computational genomics, and machine learning applications in genomics.
edX also features numerous courses on bioinformatics and genomics, designed by prestigious institutions. These courses cover a variety of topics, including data analysis techniques, genome sequencing, and personalized medicine. Learners can choose from self-paced courses or instructor-led programs that provide in-depth theoretical and practical training.
Each of these platforms allows learners to engage with course materials at their own pace, often offering certification options that can enhance professional credentials. Many courses include hands-on projects, coding exercises, and real-world case studies, equipping students with the skills needed for careers in genomics research, biotechnology, and data-driven healthcare.
In summary, FutureLearn, Coursera, and edX are major online education platforms that provide high-quality courses in bioinformatics and genomics, offering learners the flexibility to enhance their skills in these rapidly evolving fields.
FutureLearn
Genomics Courses Here:
Genomics Courses
Bioinformatics Courses Here:
Bioinformatics Courses
Coursera
Genomics Courses Here:
Genomics Courses
Bioinformatics Courses Here:
Bioinformatics Courses
EdX
Genomics Courses Here:
Genomics Courses
Bioinformatics Courses Here:
Bioinformatics Courses
Collection of Public Health Bioinformatics (PHB) Resources
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 Dockstore Resources: