From 95992191a50ac45546f05e3e21ba806674539648 Mon Sep 17 00:00:00 2001 From: Barbara Novak <19824106+bnovak32@users.noreply.github.com> Date: Mon, 20 Apr 2026 15:39:06 -0700 Subject: [PATCH] Update DECIPHER and database links - replace main DECIPHER download link with current download URL - move DECIPHER column in reference DB table to end (since it is a broken link anyway) - Update figshare links to point to the figshare main page for the document rather than the download file link (allowis user to see figshare metadata for the files) --- .../GL-DPPD-7104-C.md | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-C.md b/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-C.md index 264c1ee71..af4d47f1b 100644 --- a/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-C.md +++ b/Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-C.md @@ -68,10 +68,10 @@ Software Updates and Changes: - SILVA SSU r138: "SILVA\_SSU\_r138\_2\_2024.RData" - PR2 v4.13: "PR2\_v4\_13\_March2021.RData" - Added persistent reference links to DECIPHER databases on Figshare and replaced reference links to - DECIPHER [website](https://www2.decipher.codes/data/Downloads/TrainingSets/) - - [SILVA SSU r138](https://figshare.com/ndownloader/files/52846199) - - [UNITE v2024](https://figshare.com/ndownloader/files/52846346) - - [PR2 v4.13](https://figshare.com/ndownloader/files/46241917) + DECIPHER [website](https://decipher.codes/Downloads.html) + - [SILVA SSU r138](https://doi.org/10.6084/m9.figshare.28550993) + - [UNITE v2024](https://doi.org/10.6084/m9.figshare.28551041) + - [PR2 v4.13](https://doi.org/10.6084/m9.figshare.25797019) --- @@ -113,7 +113,7 @@ Software Updates and Changes: - [**10. Differential Abundance Testing**](#10-differential-abundance-testing) - [10a. ANCOMBC 1](#10a-ancombc-1) - [10b. ANCOMBC 2](#10b-ancombc-2) - - [10c. DESeq2 ](#10c-deseq2) + - [10c. DESeq2](#10c-deseq2) --- @@ -153,11 +153,13 @@ Software Updates and Changes: # Reference databases used -|Program used|Database|DECIPHER Link|GeneLab Figshare Link|GeneLab Download Date| -|:-----------|:------:|:------------|--------------------:|--------------------:| -|DECIPHER| SILVA SSU r138_2 | [https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2_2024.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2_2024.RData) |[SILVA_SSU_r138_2_2024.RData](https://figshare.com/ndownloader/files/52846199)| 03/06/2025 | -|DECIPHER| UNITE v2024 | [https://www2.decipher.codes/data/Downloads/TrainingSets/UNITE_v2024_April2024.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/UNITE_v2024_April2024.RData) | [UNITE_v2024_April2024.RData](https://figshare.com/ndownloader/files/52846346)| 03/06/2025 | -|DECIPHER| PR2 v4.13 | [https://www2.decipher.codes/data/Downloads/TrainingSets/PR2_v4_13_March2021.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/PR2_v4_13_March2021.RData) | [PR2_v4_13_March2021.RData](https://figshare.com/ndownloader/files/46241917)| 05/10/2024 | +|Program used|Database|GeneLab Figshare Link|GeneLab Download Date|Original DECIPHER Download Link| +|:-----------|:-------|:--------------------|:-------------------:|:------------| +|DECIPHER| SILVA SSU r138_2 | [SILVA_SSU_r138_2_2024.RData](https://doi.org/10.6084/m9.figshare.28550993)| 03/06/2025 | https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2_2024.RData | +|DECIPHER| UNITE v2024 | [UNITE_v2024_April2024.RData](https://doi.org/10.6084/m9.figshare.28551041)| 03/06/2025 | https://www2.decipher.codes/data/Downloads/TrainingSets/UNITE_v2024_April2024.RData | +|DECIPHER| PR2 v4.13 | [PR2_v4_13_March2021.RData](https://doi.org/10.6084/m9.figshare.25797019)| 05/10/2024 | https://www2.decipher.codes/data/Downloads/TrainingSets/PR2_v4_13_March2021.RData | + + --- # General processing overview with example commands