AlongkornNo/Tick-microbiome-lao-pipeline: v1.0.0 – Reproducible pipeline for cattle tick 16S rRNA microbiome analysis (Lao PDR)

Reproducibility package for the bioinformatics and statistical analysis described in the Methods section of the manuscript reporting 16S rRNA (V3–V4) amplicon sequencing of cattle tick (Rhipicephalus microplus) microbiomes from 30 specimens across six sampling sites in Lao PDR.

Contents

• Scripts 00–25, numbered in pipeline order (QIIME 2, R, and Python), from raw read QC through DADA2 denoising, taxonomy assignment, alpha/beta diversity, and figure/table generation.
• A single config.sh controlling all paths and parameters.
• Full script index and prerequisites in README.md.

Corrections applied during reconstruction

• Fixed an aggregation-order bug in the genus-level site-mean script (aggregate_genus_by_site.py / script 25): per-specimen values are now renormalized to 100% before averaging across specimens per site, matching the published table to within 0.005 percentage points.

License: MIT (see LICENSE)