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Fix broken reference database links
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asaravia-butler authored Dec 5, 2024
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Expand Up @@ -38,7 +38,7 @@ Amanda Saravia-Butler (GeneLab Data Processing Lead)

<!-- Included R packages -->
- Assay-specific suffixes were added where needed for GeneLab repo ("GLAmpSeq")
- The ITS UNITE reference database used was updated to "UNITE_v2023_July2023.RData", from http://www2.decipher.codes/Classification/TrainingSets/
- The ITS UNITE reference database used was updated to "UNITE_v2023_July2023.RData", from https://www2.decipher.codes/data/Downloads/TrainingSets/
- Several program versions were updated (all versions listed in [Software used](#software-used) below)

---
Expand Down Expand Up @@ -103,8 +103,8 @@ Amanda Saravia-Butler (GeneLab Data Processing Lead)

|Program used| Database| Relevant Links|
|:-----|:-----:|--------:|
|DECIPHER| SILVA SSU r138 | [http://www2.decipher.codes/Classification/TrainingSets/SILVA_SSU_r138_2019.RData](http://www2.decipher.codes/Classification/TrainingSets/)|
|DECIPHER| UNITE v2020 | [http://www2.decipher.codes/Classification/TrainingSets/UNITE_v2020_February2020.RData](http://www2.decipher.codes/Classification/TrainingSets/)|
|DECIPHER| SILVA SSU r138 | [https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2019.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/)|
|DECIPHER| UNITE v2023 | [https://www2.decipher.codes/data/Downloads/TrainingSets/UNITE_v2023_July2023.RData](https://www2.decipher.codes/data/Downloads/TrainingSets/)|

---

Expand Down Expand Up @@ -443,7 +443,7 @@ dna <- DNAStringSet(getSequences(seqtab.nochim))

Downloading the reference R taxonomy object:
```R
download.file( url=http://www2.decipher.codes/Classification/TrainingSets/SILVA_SSU_r138_2019.RData”, destfile=SILVA_SSU_r138_2019.RData”)
download.file( url=https://www2.decipher.codes/data/Downloads/TrainingSets/SILVA_SSU_r138_2019.RData”, destfile=SILVA_SSU_r138_2019.RData”)
```

**Parameter Definitions:**
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