01_QC_n_tax_id

Bat Shotgun Metagenomic Flow-work

This is the repository for supplementary materials for the upcoming publication

Quality Control 💎 and Taxonomic Identification 🪪

Files:

• 📑 01_Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
• ⚙️ QC_pipeline - snakemake pipeline to run fastqc & multiqc
• ⚙️ kraken2_pipeline - snakemake pipeline to run kraken2 against PlusPF database
• 📁 fastqc_reports - folder with fastqc reports:
  • 📁 {sample} - outputs are stored in folders by samples (D1-5; P1-P5):
    • 📑 {sample}_combined_R1_fastqc.html - fastqc report on forward reads
    • 📑 {sample}_combined_R2_fastqc.html - fastqc report on reverse reads
• 📁 multiqc_reports - folder with multi reports:
  • 📁 {sample} - outputs are stored in folders by samples (D1-5; P1-P5):
    • 📑 multiqc_report.html - merged forward & reverse reads multiqc report
• 📑 qc_n_tax_id.yaml - conda environment

Instruction:

• Create new environment qc_n_tax_id

conda env create -f qc_n_tax_id.yaml

System

This part of work was done on DSTU's server