Overview

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.

Syllabus

Introduction

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.

Assembly

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.

Annotation

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.

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 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.

Codon-Based Phyogenetic Trees

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.

Similar Genome Finder

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.

Protein Family Sorter

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.

Proteome Comparison

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.