This Snakemake pipeline processes ancient DNA sequencing data: it performs read preprocessing, mapping to a reference genome, duplicate removal, mitochondrial genome assembly, coverage analysis, and generates summary statistics.

🔹 Preprocessing

Adapter trimming with AdapterRemoval2

Merge overlapping reads

🔹 Mapping

Index circularized reference genome

Align reads using BWA

Realign to account for circular MT genome structure

🔹 Post-mapping

Sort BAM files

Mark duplicates using Picard

Index BAMs

🔹 Statistics and QC

Extract coverage metrics (GATK3)

Create FASTA consensus (HTSBox)

Generate summary tables for libraries and samples

1. 📦 Clone the Project

git clone https://github.com/eugeniosss/NGS_scripts

2. 🧪 Create a Snakemake Environment

conda create -n snakemake -c conda-forge -c bioconda snakemake
conda activate snakemake 

3. ▶️ Run with Snakemake (e.g., using 20 cores)

snakemake --use-conda --cores 20