Description
Aim
Next-Generation Sequencing Data Analysis using Galaxy Platform teaches practical NGS analysis using Galaxy’s web-based workflows. Learn QC, trimming, alignment, variant calling basics, RNA-seq basics, workflow building, and reproducible reporting without heavy coding.
Program Objectives
- Galaxy Basics: histories, datasets, tools, workflows, sharing.
- NGS Formats: FASTQ, BAM, VCF, GTF/GFF basics.
- QC & Trimming: quality reports and cleanup.
- Alignment: mapping reads and checking metrics.
- Variant Calling: SNP/indel workflow concepts (intro).
- RNA-seq: counts, differential expression basics (intro).
- Visualization: plots, genome browser tracks, reports.
- Reproducibility: workflow export, parameters, provenance.
- Capstone: build and share a complete Galaxy workflow.
Program Structure
Module 1: Galaxy and NGS Foundations
- Galaxy interface: histories, datasets, tool panel.
- Uploading data and managing libraries (overview).
- NGS study design: samples, replicates, metadata.
- File formats and basic validation.
Module 2: Read QC and Preprocessing
- FASTQ QC and summary reports.
- Adapter trimming and quality filtering.
- Read collapsing, contamination checks (intro).
- QC checklist for clean input reads.
Module 3: Alignment and Post-Processing
- Choosing reference genomes and indexes (overview).
- Alignment workflows and outputs (BAM).
- Sorting, indexing, duplicates (overview).
- Alignment QC: coverage, mapping rate, flags.
Module 4: Variant Calling Workflow (Intro)
- Variant calling concepts and VCF fields.
- SNP/indel calling steps (overview).
- Filtering by depth, quality, and allele balance.
- Simple annotation and variant tables (intro).
Module 5: RNA-seq Analysis Workflow (Intro)
- Read mapping for RNA-seq and gene models.
- Counting reads and normalization concepts.
- Differential expression basics (overview).
- Heatmaps, PCA, volcano plots (overview).
Module 6: Metagenomics Basics (Optional Intro)
- 16S/shotgun overview and common outputs.
- Quality filtering and taxonomic profiling (overview).
- Basic diversity concepts (intro).
- Reporting and interpretation limits.
Module 7: Workflow Building and Reproducibility
- Creating workflows from histories.
- Setting parameters and tool versions.
- Batch analysis with collections (overview).
- Sharing workflows and generating reusable templates.
Module 8: Visualization and Reporting
- Genome browser tracks and inspection (overview).
- Creating summary tables and plots.
- Exporting results and building a short analysis report.
- Good reporting: methods, parameters, QC, limitations.
Final Project
- Choose one dataset: variant calling OR RNA-seq.
- Build a complete Galaxy workflow with QC + analysis + outputs.
- Deliverables: workflow file + key plots/tables + short report.
- Submit: shared history/workflow link (or exported files) + report.
Participant Eligibility
- Students/researchers in Bioinformatics, Genetics, Biotechnology
- Beginners who want NGS analysis without heavy coding
- Basic genomics concepts helpful
Program Outcomes
- Navigate Galaxy and manage NGS datasets.
- Run QC, alignment, and core NGS workflows.
- Build reproducible Galaxy workflows and reports.
- Create a portfolio-ready Galaxy project.
Program Deliverables
- e-LMS Access: lessons, datasets, workflow templates.
- Toolkit: Galaxy workflow checklist, QC guide, report template.
- Assessment: certification after project submission.
- e-Certification and e-Marksheet: digital credentials.
Future Career Prospects
- NGS Data Analyst (Trainee)
- Bioinformatics Associate
- Genomics Research Assistant
- Clinical Research Data Assistant
Job Opportunities
- Genomics Labs/CROs: routine NGS analysis and reporting.
- Universities: genomics and transcriptomics projects.
- Biotech/Pharma: biomarker and sequencing analytics teams.
- Hospitals/Research Centers: translational genomics research groups.
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