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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 5 of 304 min read

5. Quality Control: FastQC & MultiQC

5.1 Why QC Comes Before Everything Else Running alignment or variant calling on unexamined raw data is one of the most common and consequential mistakes in NGS analysis — adapter contamination, low quality tails,…

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