RNAseq tools Fastp: Preprocessing and quality control for raw FastQ data. FastQC: Quality assessment of sequencing data after preprocessing. MultiQC: Aggregates and summarizes multiple QC reports. hisat2: High-performance alignment of RNA-Seq reads to a reference genome. samtools: Processing and manipulation of SAM/BAM files. My Note featureCounts: Quantification of gene-level expression counts. DNAseq tools BWA: Alignment of DNA sequencing reads to a reference genome. Picard: Marking duplicates and calculating alignment metrics. GATK: Variant calling and filtering to generate VCF files. vcftools: Analysis and filtering of VCF files. DNA Methylation Analysis Tools Sesame: Accurate and efficient analysis pipeline for Illumina methylation arrays. Trim Galore: Trimming of adapters and low-quality bases for methylation sequencing. Bismark: Alignment and methylation extraction from bisulfite-treated sequencing data. MethylKit: Differential methylation analysis and visualization of methylation data. DeepTools: Visualization of methylation and coverage data. methpipe: Comprehensive analysis pipeline for methylation data. Reference genome from ensembl Reference genome data