This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data.
Offered By
Bacterial Bioinformatics
University of VirginiaAbout this Course
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Intermediate Level
This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.
Approx. 14 hours to complete
English
Subtitles: English
What you will learn
Learn how to assemble a bacterial genome
Learn how to annotate a bacterial genome
Learn how to generate a phylogenetic tree from a set of bacterial genomes
Learn how to perform basic comparative analyses of a set of bacterial genomes
Shareable Certificate
Earn a Certificate upon completion
100% online
Start instantly and learn at your own schedule.
Flexible deadlines
Reset deadlines in accordance to your schedule.
Intermediate Level
This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.
Approx. 14 hours to complete
English
Subtitles: English
Offered by
University of Virginia
A premier institution of higher education, The University of Virginia offers outstanding academics, world-class faculty, and an inspiring, supportive environment. Founded by Thomas Jefferson in 1819, the University is guided by his vision of discovery, innovation, and development of the full potential of students from all walks of life. Through these courses, global learners have an opportunity to study with renowned scholars and thought leaders.
Syllabus - What you will learn from this course
1 hour to complete
Introduction
This lesson provides an introduction to PATRIC, the PathoSystems Resource Integration Center, a Bioinformatics Resource Center dedicated to supporting bacterial research. PATRIC provides comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data. PATRIC will serve as the platform for the analysis methods covered in this module.
1 hour to complete
7 videos (Total 42 min)
7 videos
History of PATRIC and the BRC program3m
PATRIC overview - tabs and information16m
Registering and logging on to PATRIC2m
PATRIC workspace-Create Shared Workspace6m
Sharing a genome with other PATRIC users4m
Copying a genome annotation job to a shared workspace3m
1 practice exercise
PATRIC overview, login, and workspace sharing30m
1 hour to complete
Assembly
This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the PATRIC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process.
1 hour to complete
7 videos (Total 49 min)
7 videos
Uploading read files to the workspace for assembly11m
Submitting reads to the Genome Assembly Service8m
Selecting assembly strategies and submitting the assembly job8m
Monitoring the assembly job and reviewing job results7m
Genome coverage in Genome Report2m
Assembly questions and getting help with problems4m
1 practice exercise
Review of genome assembly30m
2 hours to complete
Annotation
This lesson provides step-by-step instructions for annotating a genome from contigs using the PATRIC Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process.
2 hours to complete
7 videos (Total 77 min)
7 videos
Uploading contig files to the PATRIC workspace12m
Submitting a job to the PATRIC Genome Annotation Service7m
Reviewing the resulting Genome Report19m
Downloading the generated files 11m
Viewing your annotated genome in PATRIC15m
Finding help or reporting problems with the service5m
1 practice exercise
Review of genome annotation30m
2 hours to complete
Comprehensive Genome Analysis
This lesson provides step-by-step instructions for assembling, annotating, and performing an automated analysis of a genome from a set of bacterial sequence reads using the PATRIC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service.
2 hours to complete
10 videos (Total 101 min)
10 videos
Submitting a job using reads16m
Submitting contigs8m
Full Genome Report13m
Job Results11m
Assembly results11m
Annotation results12m
Viewing annotated genome12m
Finding help and citing5m
Hybrid Assembly Summary8m
1 practice exercise
Review of the Comprehensive Genome Analysis Service30m
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