Description
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.
Knowledge
- 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
Outline
- 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
Summary of User Reviews
Coursera's Informatics course has received positive reviews from many users. The course has been praised for its comprehensive curriculum and engaging lectures. Overall, users have found the course to be informative, useful, and well-structured.Key Aspect Users Liked About This Course
The course's comprehensive curriculumPros from User Reviews
- Engaging and informative lectures
- Well-structured course
- Useful content
- Great for beginners
- Good mix of theory and practice
Cons from User Reviews
- Some technical issues with the platform
- Limited interaction with instructors
- Not enough practical exercises
- Some topics could be explained better
- Lack of real-world examples
Rebecca Wattam
4.8 Raiting
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