SC2 AMD
Quality Control Reports
Video Transcript
 

SC2 AMD Quality Control Reports Transcript:

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In this video we will review:
• Viewing QC Reports
• Viewing Quality Control Metrics before releasing a run

 

New Updates: LIMS Lite is a software platform under active development. There may be small differences between the software as displayed in the video and the live version. Primary functionality of features covered in this video are current. For any additional questions on the differences, please reach out directly to the LIMS Lite team.

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LIMS Lite produces a detailed report recording all QC metrics, comments, calculations involved in the workflow, and bioinformatic tool versions used in the pipeline.
 

Click on the Results tab on the left side panel to be directed to a page listing all runs completed and in progress.
 

Click on your completed run and then on ‘View QC Report’.
 

Here you see the QC report for the entire run; both Wet-Lab Analysis details and Bioinformatics Pipeline details.
 

Let us run through the different sections of this report.
 

At the top you will see the report header, listing the run number and workflow performed, analysis point of contact or the user that performed the run, and computing environment.
 

In the next section are the Sequencing Run Notes, which lists all samples included in the workflow run, whether the sample passed or failed, and whether the sample was included in analysis.
 

Next is the Analysis Run Notes section, which displays all workflow steps and any comments that were entered during each step.
 

Sequencing Quality Controls is a review of all Quality Controls that were configured for the workflow, the workflow run value, and whether that Quality Control check passed during the run step. 
 

Click on the QC Check Requirement to see further information, including date and time of quality control check pass or failure.
 

Library Pooling and Clean Up references calculations that were made to determine volumes given during Step 10 of the workflow. 
 

These calculations are made based on the number of samples entered when beginning the workflow run.
 

Initial Dilution for Loading Calculations references calculations that were made in Step 12 of the workflow to provide pool volume and RSB volume to use.
 

The Instrument Selection section indicates whether a MiSeq or iSeq instrument was used for sequencing.
 

Bioinformatics Pipeline Analysis Details displays pipeline run date, bioinformatics tools and versions used, pipeline version and reference datasets.
 

Click MultiQC Report Workflow to view the MultiQC report, which contains default outputs from the tools within the Cecret pipeline that are preconfigured in MultiQC modules.
 

The following tools are represented in the MultiQC report:
•    Samtools
•    Pangolin
•    Kraken
•    fastp
•    FastQC
 

View Quality Control Metrics
 

Before you release your run analysis, you may view quality control metrics to determine if the run samples are of acceptable quality.
 

Click on ‘Quality Control Metrics’ next to each sample and be directed to a page displaying quantitative and qualitative quality control metrics for that sample.
 

These metrics include percent coverage of the reference genome, mean depth of coverage, and Amplicon Depth indicating depth of coverage at the lowest, median, and most highly covered amplicons.
 

Click on the Visualization tab to see Amplicon depth graphically displayed, along with additional quality scores from the FastQC Quality Control tool, such as per base quality.
 

To visualize this data at a run level, you may also reference the MultiQC report, and view this FastQC data across all samples included in the run.