🧬 What are the three stages of NGS/Omics (WGS/WES) data analysis? How do you start, and keep your workflow stress-free and organized? 📒

💡 Understanding each stage is essential for obtaining reliable and interpretable results; whether for research or clinical applications.

1️⃣ Primary analysis:

Generate DNA sequencing data from biological samples by converting sequencing instrument signals into sequence reads.

2️⃣ Secondary/Upstream analysis:

Identify DNA variants (mutations) through read alignment and variant calling.

3️⃣ Tertiary/Downstream analysis:

Annotate, filter/prioritize, classify and report variants.

🎯 Here are some great resources to get started:

1. 📚 Reading:

   1. Figure 1 in https://pubmed.ncbi.nlm.nih.gov/35395838/
   2. https://www.thermofisher.com/us/en/home/life-science/cloning/cloning-learning-center/invitrogen-school-of-molecular-biology/next-generation-sequencing/ngs-data-analysis-illumina.html

2. 🛠️ Pipelines for Secondary/Upstream analysis:

   1. nf-core/sarek: https://nf-co.re/sarek/3.5.1/
   2. nf-core/raredisease: https://nf-co.re/raredisease/2.6.0/

3. 🛠️ Tools for Tertiary/Downstream analysis:

   1. Varsome from Saphetor: https://varsome.com/ ; https://pubmed.ncbi.nlm.nih.gov/30376034/
   2. OpenCRAVAT: https://www.opencravat.org/ ; https://pubmed.ncbi.nlm.nih.gov/32228266/
   3. seqr: https://seqr.broadinstitute.org/ ; https://pubmed.ncbi.nlm.nih.gov/35266241/
   4. iobio.io: https://iobio.io/applications.html ; https://pubmed.ncbi.nlm.nih.gov/34645894/
   5. Mastermind from Genomenon, Inc: https://mastermind.genomenon.com/