Bacterial Bioinformatics

Bacterial Bioinformatics

Instructor: Rebecca Wattam

Access provided by SR University

23,379 already enrolled

8 modules

Gain insight into a topic and learn the fundamentals.

299 reviews

Intermediate level

Recommended experience

1 week to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

8 modules

Gain insight into a topic and learn the fundamentals.

299 reviews

Intermediate level

Recommended experience

1 week to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

What you'll 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

Skills you'll gain

Details to know

Assessments

8 assignments

Taught in English

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There are 8 modules in this course

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses BV-BRC, the Bacterial and Viral Bioinformatics Resource Center (merger of PATRIC, IRD and ViPR, the three former resources), as the platform for analysis. BV-BRC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. BV-BRC 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. NOTE: The exercises in this course were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides an introduction to BV-BRC, the Bacterial and Viral Resource Integration Center (formerly PATRIC), a Bioinformatics Resource Center dedicated to supporting bacterial research. BV-BRC provides comprehensive bacterial genomic data with integrated analysis tools and visualizations. BV-BRC also provides a private workspace where users can upload and analyze their own data. BV-BRC will serve as the platform for the analysis methods covered in this module. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

7 videos1 assignment

7 videos Total 42 minutes

Instructor introduction 4 minutes
History of BV-BRC and the BRC program 4 minutes
BV-BRC overview - tabs and information 17 minutes
Registering and logging on to BV-BRC 3 minutes
PATRIC workspace-Create Shared Workspace 7 minutes
Sharing a genome with other PATRIC users 4 minutes
Copying a genome annotation job to a shared workspace 4 minutes

1 assignment Total 30 minutes

PATRIC overview, login, and workspace sharing 30 minutes

This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the BV-BRC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

7 videos1 assignment

7 videos Total 49 minutes

Introduction to genome assembly 7 minutes
Uploading read files to the workspace for assembly 12 minutes
Submitting reads to the Genome Assembly Service 8 minutes
Selecting assembly strategies and submitting the assembly job 8 minutes
Monitoring the assembly job and reviewing job results 7 minutes
Genome coverage in Genome Report 2 minutes
Assembly questions and getting help with problems 5 minutes

1 assignment Total 30 minutes

Review of genome assembly 30 minutes

This lesson provides step-by-step instructions for annotating a genome from contigs using the BV-BRC Bacterial Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

7 videos1 assignment

7 videos Total 77 minutes

Introduction to genome annotation in PATRIC 5 minutes
Uploading contig files to the PATRIC workspace 12 minutes
Submitting a job to the PATRIC Genome Annotation Service 8 minutes
Reviewing the resulting Genome Report 20 minutes
Downloading the generated files 11 minutes
Viewing your annotated genome in PATRIC 15 minutes
Finding help or reporting problems with the service 5 minutes

1 assignment Total 30 minutes

Review of genome annotation 30 minutes

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 BV-BRC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

10 videos1 assignment

10 videos Total 101 minutes

Introduction to Comprehensive Genome Analysis in PATRIC 2 minutes
Submitting a job using reads 16 minutes
Submitting contigs 8 minutes
Full Genome Report 13 minutes
Job Results 12 minutes
Assembly results 12 minutes
Annotation results 12 minutes
Viewing annotated genome 12 minutes
Finding help and citing 5 minutes
Hybrid Assembly Summary 8 minutes

1 assignment Total 30 minutes

Review of the Comprehensive Genome Analysis Service 30 minutes

This lesson provides step-by-step instructions for generating a codon-based phylogentic tree from a set of genomes using the BV-BRC Codon Tree Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

9 videos1 assignment

9 videos Total 107 minutes

Introduction to codon trees 3 minutes
Creating genome groups for building codon trees 16 minutes
Submitting the tree-building job 12 minutes
Reviewing the codon tree report 12 minutes
Accessing codon tree files in the jobs folder 10 minutes
Removing problem genomes from groups 18 minutes
Using the Protein Family Sorter to improve the tree 16 minutes
Viewing the tree in FigTree 9 minutes
Finding help and citing PATRIC 11 minutes

1 assignment Total 30 minutes

Review of codon trees 30 minutes

This lesson provides step-by-step instructions for finding genomes (and associated taxonomy) in BV-BRC similar to your genome or sequences using the Similar Genome Finder Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

4 videos1 assignment

This lesson provides step-by-step instructions for using the BV-BRC Protein Family Sorter to compare presence, absence, and counts of proteins in protein families across a set of genomes. Exercises are included to enhance comprehension and build proficiency in using the tool. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

What's included

13 videos1 assignment

13 videos Total 99 minutes

Introduction to Protein Family Sorter 5 minutes
Using Global Search 8 minutes
Creating a genome group 5 minutes
Submitting a Protein Family Sorter Service analysis job 6 minutes
Protein Family Sorter tabular results 8 minutes
Filtering tabular results 9 minutes
Heatmap filtering 6 minutes
Heatmap clustering 6 minutes
Anchoring and downloading heatmap data 9 minutes
Using the Feature Table and Compare Region Viewer 14 minutes
Downloading sequences from Feature Table and viewing in the Genome Browser 11 minutes
BLASTing a genomic region 11 minutes
Protein Family Sorter summary 3 minutes

1 assignment Total 30 minutes

Review of Protein Family Sorter 30 minutes

This lesson provides step-by-step instructions for using the BV-BRC Proteome Comparison Service to compare a set of genomes against a reference genome, feature group, or FASTA file. Exercises are included to enhance comprehension and build proficiency in using the tool. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.