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lines changed Original file line number Diff line number Diff line change @@ -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
@@ -988,7 +988,7 @@ humann_databases --download utility_mapping 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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