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v3.1.0
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@fsalbeez fsalbeez released this 16 Aug 17:05
· 33 commits to main since this release
v3.1.0
470b3d3

Highlights of the 3.1.0 release:

  1. We have now included four quality control tests to evaluate assay performance in each experiment that is completed and analyzed. The first three use NTC (No Target Control) negativity, NDC (No Detection Control) negativity, and CPC (Combined Positive Control) positivity to assess each assay based on a scoring system from 0 to 1. The fourth test assesses the performance of the RNaseP (positive control used for human clinical samples) assay based on a scoring system from 0 to 1, generated by the positivity rate of clinical samples for the RNaseP assay. The results are in Assay_Level_QC_Metrics_{barcode_assignment}.csv with the explanation of the four tests in Assay_Performance__QC_Tests_{barcode_assignment}.txt.

  2. In addition to the t13_hit_output_{barcode_assignment}.csv file, the output folder also includes t13_hit_binary_output_{barcode_assignment}.csv. This file contains binary 0 and 1 results denoting negative and positive results, respectively.

  3. Previously, the Quality Control Checks conducted four checks for NTC negativity, NDC negativity, CPC positivity, and RNaseP evaluation. We have now also included a preliminary Co-Infection assessment that flags any samples that are positive for at least two assays, excluding RNaseP. This assessment has been added to the Quality_Control_Checks_{barcode_assignment}.txt.

  4. We have refined the threshold calculations by which samples are denoted positive. Now, the system first checks if any NTC sample may have high contamination (i.e. its fluorescence signal is greater than 0.5 au) for each of the assays tested. If the NTC for an assay is flagged for potential contamination, the NTC is eliminated from the threshold calculation. If all NTCs for a given assay are flagged for contamination, the program will assign keep all but one of the NTC samples and assign it a fluorescence signal of 0.5.

  5. Previously, in Quality_Control_Checks_{barcode_assignment}.txt, the NTC check incorrectly suggested that the range of typical fluorescence for an NTC sample is 0.1 – 0.4 au. It has been corrected to the range of 0.1 – 0.5 au.

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