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Metagenomics/Illumina/Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md

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@@ -29,8 +29,8 @@ Lauren Sanders (OSDR Project Scientist)
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- samtools
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- CAT
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- GTDB-Tk
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- HUMAnN3
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- MetaPhIAn3
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- HUMAnN
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- MetaPhlAn
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- In [step 14d](#14d-mag-taxonomic-classification), MAG taxonomic classification, added the new `--skip_ani_screen` argument to `gtdbtk classify_wf` to continue classifying genomes as in previous versions of GTDB-Tk, using mash and skani.
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|prodigal| 2.6.3 |[https://github.com/hyattpd/Prodigal#prodigal](https://github.com/hyattpd/Prodigal#prodigal)|
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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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|CAT| 5.2.3 |[https://github.com/dutilh/CAT#cat-and-bat](https://github.com/dutilh/CAT#cat-and-bat)|
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|Metabat2| 2.15 |[https://bitbucket.org/berkeleylab/metabat/src/master/](https://bitbucket.org/berkeleylab/metabat/src/master/)|
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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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|checkm| 1.1.3 |[https://github.com/Ecogenomics/CheckM](https://github.com/Ecogenomics/CheckM)|
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|GTDB-Tk| 2.4.0 |[https://github.com/Ecogenomics/GTDBTk](https://github.com/Ecogenomics/GTDBTk)|
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|KEGGDecoder| 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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|HUMAnN3| 3.9 |[https://huttenhower.sph.harvard.edu/humann3/](https://huttenhower.sph.harvard.edu/humann3/)|
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|MetaPhlAn3| 4.1.0 |[https://github.com/biobakery/MetaPhlAn/tree/3.0](https://github.com/biobakery/MetaPhlAn/tree/3.0)|
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|HUMAnN| 3.9 |[https://github.com/biobakery/humann](https://github.com/biobakery/humann)|
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|MetaPhlAn| 4.1.0 |[https://github.com/biobakery/MetaPhlAn](https://github.com/biobakery/MetaPhlAn)|
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