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Nutritional Programming paper across developmental stages in context of microbiome

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01- trimGalore.sh
01- trimGalore.sh
 
 
02- Sequences QA QC filtering and trimming.Rmd
02- Sequences QA QC filtering and trimming.Rmd
 
 
03- DADA2 denoising.Rmd
03- DADA2 denoising.Rmd
 
 
04- Assign Taxonomy.Rmd
04- Assign Taxonomy.Rmd
 
 
05- create a PhyloSeq object.Rmd
05- create a PhyloSeq object.Rmd
 
 
06- decontam.Rmd
06- decontam.Rmd
 
 
07- Loading andOR formating phyloseq object.Rmd
07- Loading andOR formating phyloseq object.Rmd
 
 
08- ASV QA_QC and number of taxa.Rmd
08- ASV QA_QC and number of taxa.Rmd
 
 
09- Alpha diversity.Rmd
09- Alpha diversity.Rmd
 
 
10- Beta diversity_permanova.Rmd
10- Beta diversity_permanova.Rmd
 
 
11- Beta diversity_otherDistances.Rmd
11- Beta diversity_otherDistances.Rmd
 
 
12- Taxonomic abundance.Rmd
12- Taxonomic abundance.Rmd
 
 
13- Top.four.phyla.Rmd
13- Top.four.phyla.Rmd
 
 
14- Top15_lower ASV rank.Rmd
14- Top15_lower ASV rank.Rmd
 
 
15- Shared and unique ASVs.Rmd
15- Shared and unique ASVs.Rmd
 
 
16- Venn for shared and unique ASVs, Phyla and Genera.Rmd
16- Venn for shared and unique ASVs, Phyla and Genera.Rmd
 
 
17- Metabolic reaction analysis_agora.ipynb
17- Metabolic reaction analysis_agora.ipynb
 
 
18- correlations.R
18- correlations.R
 
 
README.md
README.md
 
 
cutadapt.exe
cutadapt.exe
 
 
taxonomic_composition_devStages.xlsx
taxonomic_composition_devStages.xlsx
 
 

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NP_devStages_ampliseq

Nutritional Programming manuscript across developmental stages in context of intestinal microbiome titled: "Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): Insights across developmental stages". Paper link: https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00321-8

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