NGS Data Handling & QC — Hands-on

Gain expertise in NGS data handling and quality control—FASTQ integrity, trimming and filtering, contamination screening, alignment QC, and reproducible reports.

NGS Data Handling & Quality Control

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Session Index

Session 1 — FASTQ Integrity & Baseline QC Session 2 — Trimming, Filtering & Screening Session 3 — Alignment Metrics & Post-QC Session 4 — Mini Capstone: QC Pipeline

Session 1

Fee: Rs 6300

FASTQ Integrity & Baseline QC

Directory layout, naming, checksums & metadata capture

sha256sum MD5 CSV/TSV manifests

FASTQ structure: PHRED scores, barcodes & lanes

Theory

Baseline QC and multi-sample summaries

FastQC MultiQC seqtk

Session 2

Fee: Rs 8400

Trimming, Filtering & Screening

Adapter/quality trimming & length/complexity filters

Cutadapt Trimmomatic fastp

Contamination screening & host read removal

FastQ Screen Kraken2 BBMap

Deduplication, downsampling & QC re-evaluation

clumpify seqtk sample

Session 3

Fee: Rs 11200

Alignment Metrics & Post-QC

Short/long-read alignment & primary metrics

BWA-MEM2 Bowtie2 STAR

SAM/BAM QC, duplicates, insert size & coverage stats

samtools stats/flagstat Picard metrics mosdepth

Spike-in checks, strandedness & library complexity

RSeQC preseq

Session 4

Fee: Rs 14000

Mini Capstone: QC Pipeline

Design reproducible QC workflow from raw reads to report

Theory

Automate FastQC→trim→screen→align→metrics with provenance

Snakemake Conda/Mamba MultiQC

Deliver dashboards, artifacts & submission-ready metadata

pandas JupyterLab Quarto

PDF

NGS Data Handling & Quality Control Training | FastQC/MultiQC, Trimming, Screening & Alignment Metrics

NGS Data Handling & QC — Hands-on