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NGS Analysis30 chapters

1. Course Introduction
2. NGS Basics — Core Concepts
3. Sequencing Technologies
4. File Formats: FASTQ and FASTA
5. Quality Control: FastQC & MultiQC
6. Read Trimming: Cutadapt & fastp
7. Alignment
8. Duplicate Removal: MarkDuplicates
9. Base Quality Score Recalibration (BQSR)
10. End of Part 1 — Where We've Arrived
Coming in Part 2
Coming in Part 3

/NGS Analysis/Part 1 — Foundations: Sequencing, Raw Data, QC, Trimming & Alignment

Chapter 11 of 301 min read

Coming in Part 2

Variant Calling (GATK, DeepVariant, Sentieon, FreeBayes, Strelka), CNV Calling (CNVkit, Control FREEC, ExomeDepth, XHMM), Gene Fusion Detection (STAR Fusion, FusionCatcher, Arriba), the full Somatic Pipeline (Mutect2,…

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