Introduction

This repository contains processed 16S rRNA gene (V3-V4) sequencing data and analysis code related to below paper.

• Title: Assembly and maturation of calf gut microbiome from neonate to post puberty
• Authors: Hyun Sik Kim, Jae-Yun Lee, Tae Woong Whon, and Jin-Woo Bae
• Year: 2024

Contents

Processed data in analysis-ready format

• Processed_data.zip: A compressed zip file containing the processed data, ready for immediate analysis. It comprises the following files:
  • ASV_table.tsv: Amplicon sequencing variant (ASV) abundance table. The columns are sample names, and the rows are ASV names. Generated from DADA2 pipeline through Qiime2 platform.
  • Representative_ASV_sequences.fasta: Sequences of each ASV in FASTA format. Generated from DADA2 pipeline through Qiime2 platform.
  • Phylogenetic_tree.nwk: Newick format phylogenetic tree of ASVs, generated by q2-fragment-insertion plugin in Qiime2 platform.
  • Taxonomy.tsv: Taxonomic annotation of ASVs. Generated from Qiime2 platform.
  • Shannon_alpha_rarefaction.csv: Rarefaction curve of our data based on Shannon diversity index, generated from Qiime2 platform.
  • Metadata.tsv: Metadata containing sample information available for analysis, such as sampling time points, sample origin and host sex.

Analysis_codes containing two custom codes

• Primer_trimming.py: Python script used for trimming 338F and 805R primer from the raw reads using Cutadapt before DADA2 pipeline.

  # Example usage
  chmod 755 Primer_trimming.py # Set permissions for the script
  ./Primer_trimming.py -h # For more detail

• Draw_figures.R: R script used for generating the figures presented in our paper. All the data used for this script are in Processed_data.zip.