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.
提供方
Bacterial Bioinformatics
弗吉尼亚大学課程信息
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可分享的證書
完成後獲得證書
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中級
This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.
完成時間大約為14 小時
英語（English）
字幕：英語（English）
您將學到的內容有
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
可分享的證書
完成後獲得證書
100% 在線
立即開始，按照自己的計劃學習。
可靈活調整截止日期
根據您的日程表重置截止日期。
中級
This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.
完成時間大約為14 小時
英語（English）
字幕：英語（English）
提供方
弗吉尼亚大学
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.
教學大綱 - 您將從這門課程中學到什麼
完成時間為 1 小時
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.
完成時間為 1 小時
7 個視頻 （總計 42 分鐘）
7 個視頻
History of PATRIC and the BRC program3分鐘
PATRIC overview - tabs and information16分鐘
Registering and logging on to PATRIC2分鐘
PATRIC workspace-Create Shared Workspace6分鐘
Sharing a genome with other PATRIC users4分鐘
Copying a genome annotation job to a shared workspace3分鐘
1 個練習
PATRIC overview, login, and workspace sharing30分鐘
完成時間為 1 小時
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.
完成時間為 1 小時
7 個視頻 （總計 49 分鐘）
7 個視頻
Uploading read files to the workspace for assembly11分鐘
Submitting reads to the Genome Assembly Service8分鐘
Selecting assembly strategies and submitting the assembly job8分鐘
Monitoring the assembly job and reviewing job results7分鐘
Genome coverage in Genome Report2分鐘
Assembly questions and getting help with problems4分鐘
1 個練習
Review of genome assembly30分鐘
完成時間為 2 小時
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.
完成時間為 2 小時
7 個視頻 （總計 77 分鐘）
7 個視頻
Uploading contig files to the PATRIC workspace12分鐘
Submitting a job to the PATRIC Genome Annotation Service7分鐘
Reviewing the resulting Genome Report19分鐘
Downloading the generated files 11分鐘
Viewing your annotated genome in PATRIC15分鐘
Finding help or reporting problems with the service5分鐘
1 個練習
Review of genome annotation30分鐘
完成時間為 2 小時
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.
完成時間為 2 小時
10 個視頻 （總計 101 分鐘）
10 個視頻
Submitting a job using reads16分鐘
Submitting contigs8分鐘
Full Genome Report13分鐘
Job Results11分鐘
Assembly results11分鐘
Annotation results12分鐘
Viewing annotated genome12分鐘
Finding help and citing5分鐘
Hybrid Assembly Summary8分鐘
1 個練習
Review of the Comprehensive Genome Analysis Service30分鐘
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