Code associated with "Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population." https://doi.org/10.1111/jeb.14227
Description: These files will allow you to replicate the bioinformatic and statistical analyses we used to assess the impact of domestication on the pig gut microbiome and immune state.
The 16S_scripts folder includes files that should be used in order to process raw 16S rRNA gene sequencing data:
- Cutadapt to remove primers
- Dada2 to learn errors, dereplicate, infer ASVs, merge amplicons, make sequence tables, and assign taxonomy
- Decontam to remove contaminants, mitochondria, and chloroplasts
- Tables to create final counts and taxonomy tables
- Tree to create a phylogenetic tree
Package dependencies
| Package | Version |
|---|---|
| cutadapt | version 3.4 with Python 3.9.5 |
| dada2 | version 1.16.0 |
| decontam | version 1.10.0 |
The output will be an ASV decontaminated counts table, an ASV taxonomy table, and a phylogenetic tree. The R markdown file (16S_analyses.Rmd) will allow you to replicate any statistical analyses and visualizations for 16S rRNA gene sequencing. The excel file, fecal_metadata_Apr2022.xlsx, contains all the metadata needed for these analyses.
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The metagenomics_scripts folder includes files should be used in order to process raw shotgun metagenomic data:
- Quality filtering and trimming using Fastp
- Map sequences against reference genome
- Assemble to contigs using megahit
- Gene prediction with prodigal
- Dereplication with cd-hit
- Align to UniProt and taxonomic classification
- Annotation with EggNog, CARD, and VFDB
- Salmon gene quantification
Package dependencies
| Package | Version |
|---|---|
| MegaHit | version 1.0 |
| Prodigal | version 2.6.3 |
| cd-hit | version 4.8.1 |
| BASTA | version 1.4 with Python 3.9.5 |
| e‐mapper | version 2.1.7 |
| salmon | version 1.7.0 |
| tximport | version 1.3.9 |
Outputs will be annotation files and quantification files. The .Rmd file will allow for replication of statistical analyses and visualizations. The excel file, "dom_cat_metagenomic_metadata.xlsx," contains all the metadata associated with the samples.
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The SNP.R file along with the plink.vcf, PIG2.gds, and SNP_metadata.xlsx files can be used to replicate all SNP analyses.