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.
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Bacterial Bioinformatics
Виргинский университетОб этом курсе
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Средний уровень
This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.
Прибл. 14 часов на выполнение
Английский
Субтитры: Английский
Чему вы научитесь
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
Сертификат, ссылками на который можно делиться с другими людьми
Получите сертификат по завершении
100% онлайн
Начните сейчас и учитесь по собственному графику.
Гибкие сроки
Назначьте сроки сдачи в соответствии со своим графиком.
Средний уровень
This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.
Прибл. 14 часов на выполнение
Английский
Субтитры: Английский
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Виргинский университет
A premier institution of higher education, The University of Virginia offers outstanding academics, world-class faculty, and an inspiring, supportive environment. Founded by Thomas Jefferson in 1819, the University is guided by his vision of discovery, innovation, and development of the full potential of students from all walks of life. Through these courses, global learners have an opportunity to study with renowned scholars and thought leaders.
Программа курса: что вы изучите
1 ч. на завершение
Introduction
This lesson provides an introduction to PATRIC, the PathoSystems Resource Integration Center, a Bioinformatics Resource Center dedicated to supporting bacterial research. PATRIC provides 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. PATRIC will serve as the platform for the analysis methods covered in this module.
1 ч. на завершение
7 видео ((всего 42 мин.))
7 видео
History of PATRIC and the BRC program3мин
PATRIC overview - tabs and information16мин
Registering and logging on to PATRIC2мин
PATRIC workspace-Create Shared Workspace6мин
Sharing a genome with other PATRIC users4мин
Copying a genome annotation job to a shared workspace3мин
1 практическое упражнение
PATRIC overview, login, and workspace sharing30мин
1 ч. на завершение
Assembly
This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the PATRIC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process.
1 ч. на завершение
7 видео ((всего 49 мин.))
7 видео
Uploading read files to the workspace for assembly11мин
Submitting reads to the Genome Assembly Service8мин
Selecting assembly strategies and submitting the assembly job8мин
Monitoring the assembly job and reviewing job results7мин
Genome coverage in Genome Report2мин
Assembly questions and getting help with problems4мин
1 практическое упражнение
Review of genome assembly30мин
2 ч. на завершение
Annotation
This lesson provides step-by-step instructions for annotating a genome from contigs using the PATRIC Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process.
2 ч. на завершение
7 видео ((всего 77 мин.))
7 видео
Uploading contig files to the PATRIC workspace12мин
Submitting a job to the PATRIC Genome Annotation Service7мин
Reviewing the resulting Genome Report19мин
Downloading the generated files 11мин
Viewing your annotated genome in PATRIC15мин
Finding help or reporting problems with the service5мин
1 практическое упражнение
Review of genome annotation30мин
2 ч. на завершение
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 PATRIC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service.
2 ч. на завершение
10 видео ((всего 101 мин.))
10 видео
Submitting a job using reads16мин
Submitting contigs8мин
Full Genome Report13мин
Job Results11мин
Assembly results11мин
Annotation results12мин
Viewing annotated genome12мин
Finding help and citing5мин
Hybrid Assembly Summary8мин
1 практическое упражнение
Review of the Comprehensive Genome Analysis Service30мин
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