Outline

Utilize Galaxy tools for de novo and reference-guided genome assembly • Apply automated annotation pipelines to predict gene structures and functional elements • Validate assembly quality and assess completeness using benchmark metrics

Outline

Perform read mapping and alignment against reference genomes using industry-standard algorithms • Identify single nucleotide polymorphisms (SNPs) and structural variants from NGS data • Filter, annotate, and prioritize variants for clinical and research applications

Outline

Process raw RNA-Seq reads using Hisat2 for accurate splice-aware alignment • Quantify gene and transcript abundance with FeatureCounts and related tools • Assemble transcriptomes and discover novel isoforms from sequencing data

Outline

Design robust differential expression experiments with proper biological replicates • Execute DESeq2 workflows within Galaxy to identify significantly regulated genes • Visualize expression patterns through volcano plots, heatmaps, and PCA analyses

Outline

Perform Gene Ontology (GO) enrichment and pathway over-representation analysis • Map differentially expressed genes to biological pathways and disease associations • Interpret multi-omics results to generate actionable biological hypotheses

Outline

Construct reproducible, automated analysis pipelines using Galaxy's workflow editor • Implement best practices and optimization strategies for efficient NGS data analysis • Customize parameters and troubleshoot common bioinformatics challenges