About 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

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

Offered by

Placeholder

University of Virginia

Syllabus - What you will learn from this course

Week
1

Week 1

1 hour to complete

Introduction

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
Week
2

Week 2

1 hour to complete

Assembly

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
Week
3

Week 3

2 hours to complete

Annotation

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
Week
4

Week 4

2 hours to complete

Comprehensive Genome Analysis

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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