Linux & Bash for Bioinformatics
Zero to terminal-confident. Navigate Linux, write bash scripts, manage Conda environments, connect to HPC clusters — the foundation every other course builds on.
- Navigate Linux file system from the terminal
- Write bash scripts to automate repetitive tasks
- Install & manage tools with Conda
- Connect to HPC clusters & submit SLURM jobs
GWAS & Population Genomics
Raw genotype QC through PCA, association testing, and publication-ready Manhattan plots in R. The exact pipeline used in top-tier genetics papers.
- Sample QC: call rate, heterozygosity, HWE
- Population stratification with PCA
- Run genome-wide association in PLINK 2.0
- Manhattan & Q-Q plots in ggplot2
scRNA-seq Analysis (R/Python)
Single-cell RNA sequencing from raw counts matrix to trajectory inference — Seurat (R) and Scanpy (Python), your choice, real published datasets.
- Filter, normalise & scale a raw counts matrix
- Dimensionality reduction: PCA, UMAP, tSNE
- Cluster cells & annotate cell types
- Differential expression & trajectory inference
Variant Calling Pipeline (GATK)
GATK best-practices from FASTQ to annotated VCF — BWA alignment, HaplotypeCaller, VQSR filtering, ANNOVAR annotation.
- Align FASTQ reads with BWA-MEM
- Call SNPs & indels with GATK4 HaplotypeCaller
- Filter with VQSR & hard filtering
- Annotate with ANNOVAR & SnpEff
Molecular Docking (AutoDock Vina)
Structure-based virtual screening from protein preparation to binding pose analysis — real drug discovery targets from published studies.
- Prepare protein structures & define grid box
- Prepare ligands in PDBQT format
- Run blind & site-specific docking
- Analyse binding poses in PyMOL
MD Simulation (GROMACS)
Molecular dynamics from system setup through production runs — energy minimisation, NVT/NPT equilibration, and full trajectory analysis for publication.
- Set up protein-ligand system with CHARMM-GUI
- Energy minimisation, NVT & NPT equilibration
- Analyse RMSD, RMSF, Rg, H-bond occupancy
- Publication-ready figures with VMD & PyMOL
Thinking about the GWAS course? Try the calculator first
See exactly how many cases and controls your study design needs — the same calculation we teach in the course, running right here.
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Drug Discovery Pipeline — Full Track Bundle
All four drug discovery courses in one programme — the complete journey from variant to validated hit.
- Linux & Bash for Bioinformatics (₹999)
- Variant Calling Pipeline — GATK (₹3,499)
- Molecular Docking — AutoDock Vina (₹3,499)
- MD Simulation — GROMACS (₹3,999)
Looking for an in-person intensive workshop?
OmixLab also delivers 2–3 day hands-on workshops in Ahmedabad, Dubai, and at universities across SE Asia and Africa. Small batches. Real datasets. Immersive learning.