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Final updates
- Updated software versions to latest possible - Specify separate tidyverse instead of the tidyverse collection for more granular software versions - Add final pipeline approval date
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‎Metagenomics/Illumina/Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-B.md‎

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**Date:** April MM, 2026
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**Date:** April 3, 2026
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**Revision:** B
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**Document Number:** GL-DPPD-7107
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| Program | Version | Relevant Links |
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| :----------- | :-----: | :------------------------------------------------------------------------------------------------------------------------------------------------- |
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| BBTools | 39.80 | [https://bbmap.org/](https://bbmap.org/) |
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| BBTools | 39.81 | [https://bbmap.org/](https://bbmap.org/) |
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| bit | 1.13.15 | [https://github.com/AstrobioMike/bioinf_tools#bioinformatics-tools-bit](https://github.com/AstrobioMike/bioinf_tools#bioinformatics-tools-bit) |
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| bowtie2 | 2.5.5 | [https://bowtie-bio.sourceforge.net/bowtie2/index.shtml](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml) |
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| CAT | 5.2.3 | [https://github.com/MGXlab/CAT_pack](https://github.com/MGXlab/CAT_pack) |
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| CheckM | 1.1.3 | [https://github.com/Ecogenomics/CheckM](https://github.com/Ecogenomics/CheckM) |
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| CAT | 5.3 | [https://github.com/MGXlab/CAT_pack](https://github.com/MGXlab/CAT_pack) |
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| CheckM | 1.2.5 | [https://github.com/Ecogenomics/CheckM](https://github.com/Ecogenomics/CheckM) |
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| fastp | 1.3.1 | [https://github.com/OpenGene/fastp](https://github.com/OpenGene/fastp) |
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| FastQC | 0.12.1 | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) |
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| GTDB-Tk | 2.4.0 | [https://github.com/Ecogenomics/GTDBTk](https://github.com/Ecogenomics/GTDBTk) |
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| GTDB-Tk | 2.6.1 | [https://github.com/Ecogenomics/GTDBTk](https://github.com/Ecogenomics/GTDBTk) |
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| HUMAnN | 3.9 | [https://github.com/biobakery/humann](https://github.com/biobakery/humann) |
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| Kaiju | 1.10.1 | [https://bioinformatics-centre.github.io/kaiju/](https://bioinformatics-centre.github.io/kaiju/) |
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| KEGG-Decoder | 1.2.2 | [https://github.com/bjtully/BioData/tree/master/KEGGDecoder#kegg-decoder](https://github.com/bjtully/BioData/tree/master/KEGGDecoder#kegg-decoder) |
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| KEGG-Decoder | 1.3 | [https://github.com/bjtully/BioData/tree/master/KEGGDecoder#kegg-decoder](https://github.com/bjtully/BioData/tree/master/KEGGDecoder#kegg-decoder) |
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| KOFamScan | 1.3.0 | [https://github.com/takaram/kofam_scan#kofamscan](https://github.com/takaram/kofam_scan#kofamscan) |
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| Kraken2 | 2.1.6 | [https://github.com/DerrickWood/kraken2](https://github.com/DerrickWood/kraken2) |
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| KrakenTools | 1.2 | [https://ccb.jhu.edu/software/krakentools/](https://ccb.jhu.edu/software/krakentools/) |
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| Kraken2 | 2.17.1 | [https://github.com/DerrickWood/kraken2](https://github.com/DerrickWood/kraken2) |
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| KrakenTools | 1.2.1 | [https://ccb.jhu.edu/software/krakentools/](https://ccb.jhu.edu/software/krakentools/) |
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| Krona | 2.8.1 | [https://github.com/marbl/Krona/wiki](https://github.com/marbl/Krona/wiki) |
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| MEGAHIT | 1.2.9 | [https://github.com/voutcn/megahit#megahit](https://github.com/voutcn/megahit#megahit) |
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| MetaBAT | 2.15 | [https://bitbucket.org/berkeleylab/metabat/src/master/](https://bitbucket.org/berkeleylab/metabat/src/master/) |
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| MetaBAT | 2.18 | [https://bitbucket.org/berkeleylab/metabat/src/master/](https://bitbucket.org/berkeleylab/metabat/src/master/) |
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| MetaPhlAn | 4.1.0 | [https://github.com/biobakery/MetaPhlAn](https://github.com/biobakery/MetaPhlAn) |
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| MultiQC | 1.27.1 | [https://multiqc.info/](https://multiqc.info/) |
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| Prodigal | 2.6.3 | [https://github.com/hyattpd/Prodigal#prodigal](https://github.com/hyattpd/Prodigal#prodigal) |
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| samtools | 1.22.1 | [https://github.com/samtools/samtools#samtools](https://github.com/samtools/samtools#samtools) |
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| samtools | 1.23.1 | [https://github.com/samtools/samtools#samtools](https://github.com/samtools/samtools#samtools) |
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| SPAdes | 4.2.0 | [https://github.com/ablab/spades](https://github.com/ablab/spades) |
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| R | 4.5.3 | [https://www.r-project.org](https://www.r-project.org) |
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| decontam | 1.28.0 | [https://www.bioconductor.org/packages/release/bioc/html/decontam.html](https://www.bioconductor.org/packages/release/bioc/html/decontam.html) |
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| dplyr | 1.2.0 | [https://dplyr.tidyverse.org](https://dplyr.tidyverse.org) |
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| ggplot2 | 4.0.2 | [https://ggplot2.tidyverse.org](https://ggplot2.tidyverse.org) |
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| htmlwidgets | 1.6.4 | [http://www.htmlwidgets.org](http://www.htmlwidgets.org) |
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| glue | 1.8.0 | [https://glue.tidyverse.org](https://glue.tidyverse.org) |
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| pavian | 1.2.0* | [https://github.com/fbreitwieser/pavian](https://github.com/fbreitwieser/pavian) |
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| htmlwidgets | 1.6.4 | [http://www.htmlwidgets.org](http://www.htmlwidgets.org) |
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| magrittr | 2.0.5 | [https://magrittr.tidyverse.org](https://magrittr.tidyverse.org) |
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| pavian | 1.2.0* | [https://github.com/fbreitwieser/pavian](https://github.com/fbreitwieser/pavian) |
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| pheatmap | 1.0.13 | [https://cran.r-project.org/package=pheatmap](https://cran.r-project.org/package=pheatmap) |
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| phyloseq | 1.54.0 | [https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html) |
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| plotly | 4.12.0 | [https://plotly-r.com](https://plotly-r.com) |
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| purrr | 1.2.1 | [https://purrr.tidyverse.org](https://purrr.tidyverse.org) |
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| readr | 2.2.0 | [https://readr.tidyverse.org](https://readr.tidyverse.org) |
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| scales | 1.4.0 | [https://scales.r-lib.org](https://scales.r-lib.org) |
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| stringr | 1.6.0 | [https://stringr.tidyverse.org](https://stringr.tidyverse.org) |
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| tibble | 3.3.1 | [https://tibble.tidyverse.org](https://tibble.tidyverse.orgtext) |
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| tidyr | 1.3.2 | [https://tidyr.tidyverse.org](https://tidyr.tidyverse.orgtext) |
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#### 3a. Load libraries
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```R
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library(glue)
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# load libraries
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library(htmlwidgets)
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library(pavian)
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library(pheatmap)
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library(phyloseq)
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# load tidyverse libraries
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library(dplyr)
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library(ggplot2)
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library(glue)
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library(magrittr)
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library(plotly)
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library(tidyverse)
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library(purrr)
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library(readr)
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library(scales)
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library(stringr)
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library(tibble)
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library(tidyr)
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```
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#### 3b. Define Custom Functions

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