University of Virginia - Bacterial Bioinformatics
- Offered byCoursera
- Public/Government Institute
Bacterial Bioinformatics at Coursera Overview
Duration | 14 hours |
Total fee | Free |
Mode of learning | Online |
Difficulty level | Intermediate |
Official Website | Explore Free Course  |
Credential | Certificate |
- Overview
- Highlights
- Course Details
- Curriculum
Bacterial Bioinformatics at Coursera Highlights
- Earn a shareable certificate upon completion.
- Flexible deadlines according to your schedule.
Bacterial Bioinformatics at Coursera Course details
- 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.
- Course participants will gain skills needed to do comparative analysis of bacterial genomes, starting with raw sequence data.The lessons in the first module cover genome assembly, annotation, phylogenetic tree construction, and protein family / proteome comparisons. Each lesson builds on the previous, creating a complete baseline analysis workflow.
Bacterial Bioinformatics at Coursera Curriculum
Introduction
Instructor introduction
History of PATRIC and the BRC program
PATRIC overview - tabs and information
Registering and logging on to PATRIC
PATRIC workspace-Create Shared Workspace
Sharing a genome with other PATRIC users
Copying a genome annotation job to a shared workspace
PATRIC overview, login, and workspace sharing
Assembly
Introduction to genome assembly
Uploading read files to the workspace for assembly
Submitting reads to the Genome Assembly Service
Selecting assembly strategies and submitting the assembly job
Monitoring the assembly job and reviewing job results
Genome coverage in Genome Report
Assembly questions and getting help with problems
Review of genome assembly
Annotation
Introduction to genome annotation in PATRIC
Uploading contig files to the PATRIC workspace
Submitting a job to the PATRIC Genome Annotation Service
Reviewing the resulting Genome Report
Downloading the generated files
Viewing your annotated genome in PATRIC
Finding help or reporting problems with the service
Review of genome annotation
Comprehensive Genome Analysis
Introduction to Comprehensive Genome Analysis in PATRIC
Submitting a job using reads
Submitting contigs
Full Genome Report
Job Results
Assembly results
Annotation results
Viewing annotated genome
Finding help and citing
Hybrid Assembly Summary
Review of the Comprehensive Genome Analysis Service
Codon-Based Phyogenetic Trees
Introduction to codon trees
Creating genome groups for building codon trees
Submitting the tree-building job
Reviewing the codon tree report
Accessing codon tree files in the jobs folder
Removing problem genomes from groups
Using the Protein Family Sorter to improve the tree
Viewing the tree in FigTree
Finding help and citing PATRIC
Review of codon trees
Similar Genome Finder
Launching a search using a genome
Launching a search using a contig file
Launching a search using a fastq file
Finding help and citing PATRIC
Review of Similar Genome Finder
Protein Family Sorter
Introduction to Protein Family Sorter
Using Global Search
Creating a genome group
Submitting a Protein Family Sorter Service analysis job
Protein Family Sorter tabular results
Filtering tabular results
Heatmap filtering
Heatmap clustering
Anchoring and downloading heatmap data
Using the Feature Table and Compare Region Viewer
Downloading sequences from Feature Table and viewing in the Genome Browser
BLASTing a genomic region
Protein Family Sorter summary
Review of Protein Family Sorter
Proteome Comparison
Introduction to Proteome Comparison
Selecting parameters
Selecting a reference genome
Using a feature group or FASTA file as input
Using a feature group as the reference
Using a FASTA file as the reference
Selecting the genomes to use for the comparison
3 flavors of reference genomes
Reviewing the output job results
Citing PATRIC and getting help
Summary of analysis of two assembly strategies
Review of Proteome Comparison
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