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bnovak32 merged 1 commit into from
Apr 20, 2026
+12 −10
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Update DECIPHER and database links #200

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22 changes: 12 additions & 10 deletions Amplicon/Illumina/Pipeline_GL-DPPD-7104_Versions/GL-DPPD-7104-C.md
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Expand Up @@ -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)

---

Expand Down Expand Up @@ -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)

---

Expand Down Expand Up @@ -153,11 +153,13 @@ Software Updates and Changes:
# Reference databases used
<update figshare links once the updated DBs are downloaded>

|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&nbsp;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&nbsp;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
Expand Down