Udemy - Building and querying a kraken2 database


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Udemy - Building and querying a kraken2 database


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Get Bonus Downloads Here.url 204.8 B
001 Introduction.mp4 37.7 MB
002 Installing kraken2.mp4 26.7 MB
003 Kraken2 database and query input.mp4 61.9 MB
004 How to use sequences from outside NCBI.mp4 18.3 MB
005 The kraken2 algorithm.mp4 35.7 MB
006 How many sequences to add to your database_.mp4 19.5 MB
30356818-kraken2-install.txt 307.2 B
001 SIBO database overview.mp4 17.2 MB
002 Adding genomes to the SIBO kraken2 database.mp4 97.8 MB
003 Other types of kraken2 databases and libraries.mp4 12.8 MB
004 Building the database.mp4 44.1 MB
005 What is in the database_ kraken2-inspect.mp4 43.1 MB
006 A note on classification.mp4 27.6 MB
001 Downloading SIBO data sets from the SRA database.mp4 34.7 MB
002 Running a query and interpreting output.mp4 47.2 MB
003 Interpreting a kraken2 report.mp4 102.3 MB
004 Querying the SIBO database with a Parkinson's gut sample.mp4 62 MB
005 Visualizing results with Pavian.mp4 62.1 MB
001 kraken2 environmental variables.mp4 45.6 MB
002 MPA style reports.mp4 35.3 MB
003 Summary and Conclusion, further ideas and other metagenomics tools.mp4 21.3 MB
Bonus Resources.txt 307.2 B


Building and querying a kraken2 database


MP4 | Video: h264, 1280x720 | Audio: AAC, 44.1 KHz
Language: English | Size: 852 MB | Duration: 2h 0m
A useful Next Generation Sequencing (NGS) Metagenomics tool
What you'll learn
how to design, build and query a kraken2 database
how to classify Next Generation Sequence reads to a metagenomics database
how to visualize a classification report in Pavian
basic Linux knowledge
understand basic shell commands
Kraken2 is a well-known Next Generation Sequencing (NGS) metagenomics classification tool. It is used widely in scientific research. With kraken2 you can build a database using whole genome sequences to classify read sequences against to identify unknown samples. It is easy to use and performs very rapid sample classification. Kraken2 has application in biology, medical research and even geology.

In this video we will see a general overview of the algorithm behind the kraken2 database language. Then, we will do a hands-on example whereby we download read data sets from the SRA database from NCBI (the National Center for Biotechnology Information) and classify them against the database that we have built. We will also look at the Pavian visualization software which presents a graphical overview of our results (i.e. Stankey diagram). Figures made in this program can also be used for publication purposes.

Students of this course are mainly either biology or medical students or researchers. Some knowledge of Linux is required to take the course, but there are only few commands that need clarification, but they will be explained in detail.

In total, it is worthwhile learning the skills used in this course, which can give you the edge in metagenomics research and analysis.

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