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

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@@ -979,7 +979,7 @@ KEGG-decoder -v interactive -i MAG-level-KO-annotations_GLmetagenomics.tsv -o MA
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## Read-based processing
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### 16. Taxonomic and functional profiling
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The following uses the `humann3` and `metaphlan3` reference databases downloaded on 26-Sept-2020 as follows:
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The following uses the `humann` and `metaphlan` reference databases downloaded on 13-Jun-2024 as follows:
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```bash
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humann_databases --download chocophlan full
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metaphlan --install
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```
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#### 16a. Running humann3 (which also runs metaphlan3)
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#### 16a. Running humann (which also runs metaphlan)
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```bash
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# forward and reverse reads need to be provided combined if paired-end (if not paired-end, single-end reads are provided to the --input argument next)
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cat sample-1_R1_filtered.fastq.gz sample-1_R2_filtered.fastq.gz > sample-1-combined.fastq.gz

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