Tools

Individual tool guides with installation instructions and runnable examples.

• Quality Control
  • FastQC
  • fastp
  • MultiQC
  • NanoPlot
  • pycoQC
  • Chopper
• Alignment
  • BWA-MEM2
  • minimap2
  • Bowtie2
  • STAR
• SAM/BAM Processing
  • SAMtools
  • Sambamba
  • Picard
  • deepTools
• Interval Operations
  • BEDTools
• Genome Assembly
  • Flye
  • Canu
  • SPAdes
  • Unicycler
  • Medaka
• Assembly Quality Control
  • QUAST
  • BUSCO
• Genome Annotation
  • Bakta
  • Prokka
  • BRAKER
• Variant Calling
  • GATK
  • Clair3
  • FreeBayes
  • DeepVariant
• Variant Annotation
  • VEP (Variant Effect Predictor)
  • SnpEff
• Variant Processing
  • BCFtools
• Quantification
  • kallisto
  • Salmon
  • featureCounts
  • HTSeq
• Differential Expression
  • DESeq2
  • edgeR
• Single-Cell Analysis
  • Cell Ranger
  • STARsolo
  • Seurat
  • Scanpy
• Metagenomics
  • Kraken2
  • Bracken
  • Krona
• Epigenomics
  • MACS2
  • Bismark
• Basecalling
  • Dorado
  • Guppy
• Data Access
  • SRA Toolkit
  • Entrez Direct
• Visualization
  • IGV