Overview

This is documentation to help you analyze a single sample in IDseq. We’ll walk through the user interface, pipeline results, run quality interpretation, and Sample Report interpretation in the upcoming sections.

The main views you will use to interpret your data:

• Project Page will help you find your samples and see the QC metrics for all your samples at once.
• Pipeline Details will dive into analyzing the quality of the reads in detail.
• Single Sample Report Table will help you understand how to interpret the matches found.
• Sample Report Taxon Tree will visualize the data to draw your eye to important matches.
• Filtering helps you filter out noise.
• Coverage Visualization will dive into how well the results match against the reference genome.
• Download will allow you to download the data to do any additional analysis you may to do offline.