Reproducible Analysis, Scientific Reporting and Portfolio Development

• End-to-end guided NGS project in your chosen domain
• Reproducible environment & workflow design guidance
• Full analysis pipeline support, start to finish
• Scientific report writing & data visualization coaching
• Final presentation & portfolio-ready project repository
• Project Completion Certificate
• 12–16 weeks of weekly 1:1 mentoring (18–24 hrs)

Somatic Variant Analysis and Biological Interpretation

• Cancer biology & sequencing strategies (tumor-normal design)
• Somatic variant calling & filtering
• Manual variant review in IGV
• Copy-number & structural variant concepts
• Cancer databases (COSMIC, ClinVar, OncoKB, CIViC)
• Driver prioritization & mutational signatures
• Certificate of Completion
• 12 live sessions, 1.5 hrs weekly

16S Amplicon Sequencing and Community Analysis

• 16S rRNA amplicon sequencing fundamentals
• Data processing with QIIME 2 / DADA2 concepts
• ASV/OTU generation & taxonomic classification
• Alpha and beta diversity analysis
• Community composition visualization
• Biological interpretation & reporting
• Certificate of Completion
• 10 live sessions, 1.5 hrs weekly

From Raw Reads to Differential Gene Expression

• RNA-seq experimental design & quality control
• Splice-aware alignment (STAR / HISAT2)
• Gene-level quantification & count matrices
• Differential expression analysis in R with DESeq2
• PCA, volcano plots & expression heatmaps
• Functional enrichment (Gene Ontology, pathway analysis)
• Certificate of Completion
• 10 live sessions, 1.5 hrs weekly

Alignment, BAM Processing and Variant Fundamentals

• Reference genomes & read alignment (BWA, Bowtie2)
• SAM/BAM processing with SAM tools
• Coverage & mapping-quality analysis
• Genome browsing & visual review in IGV
• Introductory variant calling and VCF interpretation
• Certificate of Completion
• 8 live sessions, 1.5 hrs weekly

Linux, FASTQ Quality Control and Read Processing

• Linux command-line fundamentals & file management
• Bash text processing (grep, awk, sed, sort, uniq)
• Downloading public sequencing data (SRA / ENA)
• FastQC & MultiQC quality assessment
• Adapter trimming and read filtering
• Reproducible project workflow & scripting
• Certificate of Completion
• 8 live sessions, 1.5 hrs weekly

Sequencing Technologies, Data Formats and Quality Concepts

• NGS platforms & sequencing technologies (Illumina, Nanopore, PacBio)
• Library preparation & sequencing workflow
• Core NGS file formats: FASTQ, SAM, BAM, VCF, BED, GFF/GTF
• Quality, depth & coverage concepts
• Public repositories & metadata (SRA, ENA, GEO)
• Certificate of Completion
• 6 live sessions, 1.5 hrs weekly

Sanger Sequencing, Quality Assessment and Sequence Preparation

• Hands-on training with real sequencing datasets
• Sanger sequencing fundamentals & chromatogram reading
• Phred quality scores and quality-region interpretation
• Sequence alignment and consensus building
• FASTA formatting and sequence preparation
• BLAST analysis and biological interpretation
• Certificate of Completion
• 4 live sessions, 1.5 hrs every Saturday

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