Udemy - Building and querying a kraken2 database

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[ TutSala.com ] Udemy - Building and querying a kraken2 database
  • Get Bonus Downloads Here.url (0.2 KB)
    • ~Get Your Files Here ! 01 - Introduction
    • 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 (0.3 KB)
    02 - Building the SIBO kraken2 database
    • 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)
    03 - Querying the database
    • 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 (62.0 MB)
    • 005 Visualizing results with Pavian.mp4 (62.1 MB)
    04 - Extra kraken2 material
    • 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 (0.3 KB)

Description

Building and querying a kraken2 database



https://TutSala.com

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
Requirements
basic Linux knowledge
understand basic shell commands
Description
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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Udemy - Building and querying a kraken2 database

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852.9 MB
seeders:4
leechers:1
Udemy - Building and querying a kraken2 database

Torrent hash: 9607BF7749271EEEBD8D48A8C6311AF6BC544FF3