Describe a typical NGS data analysis pipeline and its key steps.

A typical NGS data analysis pipeline includes: 1) Quality control - assess raw read quality using FastQC, check for adapter contamination and base quality scores. 2) Preprocessing - trim adapters and low-quality bases using Trimmomatic or Cutadapt. 3) Alignment - map reads to reference genome using BWA, Bowtie2, or STAR (for RNA-Seq). 4) Post-alignment processing - sort, index, mark duplicates using SAMtools and Picard. 5) Variant calling - identify SNPs/indels using GATK, FreeBayes, or application-specific tools. 6) Annotation - annotate variants with functional impact using ANNOVAR, VEP, or SnpEff. 7) Visualization and interpretation - use IGV, R/Bioconductor for downstream analysis.