Building and querying a kraken2 database

A useful Next Generation Sequencing (NGS) Metagenomics tool

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.

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.

Course Content

  • Introduction –> 6 lectures • 33min.
  • Building the SIBO kraken2 database –> 6 lectures • 32min.
  • Querying the database –> 5 lectures • 41min.
  • Extra kraken2 material –> 3 lectures • 14min.

Building and querying a kraken2 database

Requirements

  • 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.