How to use Kraken results downstream?

Prepare Kraken Results

• Make sure you have Kraken results files (.output and .report) accessible for analysis. These files are critical for downstream processes.

 

• Organize the files in a directory that's easy to navigate, ensuring there are no naming conflicts with other projects.

Parse the Kraken Output

• Use a scripting language like Python to parse the Kraken output. Libraries such as Pandas can be helpful for handling tabular data efficiently.

 

• Extract relevant information such as sequence IDs, taxonomic classifications, and confidence scores from the Kraken output.

Generate Visualizations

• Consider using visualization tools like Krona or Graphviz to create an interactive visual representation of the taxonomic classification. These visuals can aid in the quick identification of dominant organisms.

 

• Ensure that the visualizations are clear and tailored to the specific research questions or audience by adjusting parameters such as color schemes and node sizes.

Conduct Statistical Analysis

• Import the parsed data into statistical software or a programming environment like R or Python to perform abundance calculations and diversity indices.

 

• Apply statistical methods to understand the structure of the microbial community, looking for patterns, clusters, or anomalies in the data.

Integrate with Other Data Sources

• Combine Kraken results with additional data sources such as gene expression profiles, environmental metadata, or clinical data to provide context to the microbial profiles.

 

• Utilize data integration platforms or custom scripts to handle this data consolidation, ensuring consistent formatting and data integrity.

Prepare a Summary Report

• Create a comprehensive report summarizing the analysis, including key findings, visualizations, and a discussion of implications.

 

• Ensure that the report is logically structured, making it easy for stakeholders to understand and interpret the results. Provide actionable insights or recommendations based on the analysis.