v5.4.2

Highlights of the 5.4.2 release
Previously, there were issues with the samples being plotted in an ambiguous order on all heatmaps. This version resolves this concern. Now, the heatmaps plot the samples in the order of their list in the assignment sheet.

v5.4.1

Highlights of the 5.4.1 release:
Previously, there were issues with the QC Scores per Assay csv file saving when this repository was cloned and ran on Windows operating system. This version resolves these bugs.

v5.4.0

Highlights of the 5.4.0 release
Previously, there was an issue when analyzing runs combining assays from RVP with BBP Panel 1 and Panel 2 assays. This version has resolved this issue.

Previously, there was an issue with plotting heatmaps with duplicate assays and fewer than 192 samples (i.e. duplicated samples). This version has resolved this issue wherein the median of duplicated assays’ data is taken for the same sample. Additionally, heatmaps are now successfully generated with a (1x1) format.

Updated installation requirements:
To generate the Redcap file necessary for data storage at clinical partner sites, you must add the command-line argument REDCAP to the end of your run command. For example, on a macOS system, this would be:

• python3 analyze_run.py 1.8_Mean REDCAP

• python3 analyze_run.py 3_SD REDCAP

The Redcap file will be generated in the RESULTS sub-folder within the output folder.

To most accurately capture the assay and sample invalidity status in the RESULTS Excel file and the REDCAP file, it is recommended that you name assays exactly as listed below (case-insensitive, but underscores and dashes must match):

• BBP P1 assays: CCHFV, EBOV, HIV_1, HIV_2, LASV, MBV, MPOX_DNA, PF_3_DNA, WNV, YFV, RNASEP_P1

• BBP P2 assays: CHI, DENV, HBV_DNA, HCV, HTV, MMV, ONN, RBV, RVFV, SYPH_DNA, ZIKV, NPV, RNASEP_P2

• RVP assays: SARS_COV-2, HCOV_HKU1, HCOV_NL63, HCOV_OC43, FLUAV, FLUBV, HMPV, HRSV, HPIV_3, RNASEP_RVP

• Control assay: no_crRNA

To generate accurate assay performance evaluations, it is recommended that sample names must end with _RVP, _P1, or _P2, corresponding to the panels for which you hope to test the sample against.

v5.3.0

Highlights of the 5.3.0 release
This release updates the REDCap file to now include the threshold used and the software version.

v5.2.2

Highlights of the 5.2.2 release
This release resolves the bugs with viral assays containing underscores.

v5.2.1

Highlights of the 5.2.1 release
This release includes Nipah virus as part of the designated BBP Panel 2 viral assays. This update is necessary for REDCAP data storage.

v5.2.0

Highlights of the 5.2.0 release

1. This release has resolved the following issues with the formatting of the REDCAP file:
2. The date is now compiled as DD/MM/YYYY.
3. The contaminated NTC check now correctly codes NTC samples with background fluorescence signal greater than 0.5 a.u as a 6 in the REDCAP file.
4. Positive samples are coded as 1 not 1.0.
5. The merging of the same sample ran on different panels is now done by verifying which panel the viral assay belongs to.

v5.1.1

Highlights of the 5.1.1 release
This release has resolved issues with REDCAP file formatting, specifically regarding bugs with coding samples that are negative for RNaseP.

v5.1.0

Highlights of the 5.1.0 release

1. Add REDCAP as an additional command line argument when running the code, if you are interested in generating the REDCAP. For example, python3 -i analyze_run.py 3_SD REDCAP
2. Metadata formatting is now added into the REDCAP csv file
3. The ‘Assay Valid?’ row is added to all files, with VALID or INVALID as the cell value. Previously, this row was only appended to the RESULTS Excel file if there were invalid assays.

v5.0.0

Highlights of the 5.0.0 release
This release has built in redcap_builder.py to generate Redcap_{IFC_barcode).csv for Redcap data integration at partner sites.