Genome Assembly, Variant Calling & Annotation — Hands-on

Gain expertise in genome assembly, variant calling, and functional annotation with end-to-end, reproducible hands-on labs.

Genome Assembly, Variant Calling & Annotation

Session Index

Session 1

Fee: Rs 6300

Assemblies & Polishing

De novo vs reference-guided assembly strategies

Theory

Short/long-read assemblers & hybrid approaches

SPAdes MEGAHIT Flye Canu

Polishing, scaffolding & assembly QC

Pilon Racon QUAST BUSCO

Session 2

Fee: Rs 8400

Mapping & Preprocessing

Read alignment for short/long reads; primary metrics

BWA-MEM2 Bowtie2 minimap2

SAM/BAM processing: sorting, indexing, duplicates, calibration

samtools Picard GATK BQSR

Coverage, insert-size & library complexity checks

mosdepth RSeQC preseq

Session 3

Fee: Rs 11200

Variant Calling & Annotation

SNP/indel callers, joint calling & cohort VCFs

GATK HaplotypeCaller bcftools FreeBayes

Filtering, normalization & quality models

GATK VQSR Hard filters bcftools norm

Functional effects & structural variants

SnpEff VEP Manta/Delly

Session 4

Fee: Rs 14000

Mini Capstone: AVA Pipeline

Design end-to-end assembly→variants→annotation workflow

Theory

Automate mapping, calling, filtering & reports

Snakemake Conda/Mamba MultiQC

Deliver VCFs, annotated tables & dashboards

pandas JupyterLab Quarto

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Genome Assembly, Variant Calling & Annotation Training | GATK, SPAdes, VCF, SnpEff/VEP