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.

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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.

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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.

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Reference genome from ensembl

Reference genome data