A practical research toolkit for graduate students and professionals analyzing SARS-CoV-2 mutations, especially targeting RdRp-related antiviral resistance.

What This Handbook Offers

This concise, step-by-step guide walks you through the complete workflow of SARS-CoV-2 mutation analysis, focusing on the RNA-dependent RNA polymerase (nsp12) gene which is a critical target for antiviral drugs like Remdesivir, Molnupiravir, and Favipiravir.

Graduate students researchers, or lab analyst, this practical resource will help you go from:

🔹 Raw FASTQ files → 🔹 Consensus FASTA → 🔹 Motif extraction → 🔹 Mutation calling → 🔹 Publishable dataset

What’s Inside?

• About total 07 pages of clear instructions with command-line workflows
• Compatible pipelines for Oxford Nanopore & Illumina data
• Tools: minimap2, medaka, bwa, ivar, seqkit, mafft, trimal, Biopython, Pandas
• Python scripts for:
  • Mutation extraction by motif (A, C, F, G)
  • Frequency analysis & sample tracking
  • Combined mutation table generation
• Sample folder structure, and actual files, troubleshooting tips, and final archiving guidance
• Optional validation workflow using Nextclade

Who Is This For?

• Graduate students & researchers in virology, bioinformatics, genomics
• Public health & academic labs performing SARS-CoV-2 variant surveillance
• Biotech teams evaluating antiviral resistance
• Educators teaching real-world viral genomics workflows

Bonus Features

• DOI-linked version (Zenodo)
• Reproducible scripts & structured outputs CSV, FASTA, etc.
• License: Creative Commons BY 4.0 — use it, cite it, adapt it!

Start building high-confidence, publication-ready SARS-CoV-2 mutation datasets today. https://tahirhb.gumroad.com/l/zxuxs