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Bioinformatics Tools Reference

A curated catalog of commonly used tools organized by workflow step. Each entry links to the official source so you can evaluate and install what fits your pipeline. Some tools listed here are developed by the same team behind this tutorial site.

Quality Control & Preprocessing

QC is the first step in nearly every pipeline. These tools help you assess raw read quality, detect adapter contamination, and trim/filter reads before downstream analysis.

ToolPlatformDescription
FastQC Desktop / CLI Widely-used QC report generator for FASTQ files — provides per-base quality, GC content, adapter content, and overrepresented sequence analysis.
MultiQC CLI Aggregates results from many tools (FastQC, STAR, Salmon, etc.) into a single interactive HTML report. Essential for multi-sample projects.
fastp CLI All-in-one preprocessor: quality trimming, adapter removal, filtering, and QC reporting in one pass. Very fast (multi-threaded C++).
Cutadapt CLI Flexible adapter and quality trimming tool with a rich filtering API. Great for non-standard adapter schemes.
Trimmomatic CLI (Java) Illumina-specific trimming with sliding-window quality filtering. Mature and widely cited.
FastQLab Mobile (Android / iOS) On-device FASTQ quality control for quick field or classroom use. Same panels you learn to read in FastQC, when a workstation is not available.
Read Alignment

Aligners map sequencing reads to a reference genome or transcriptome. The choice depends on your experiment type (DNA vs RNA), speed requirements, and memory constraints.

ToolTypeDescription
BWA-MEM2 DNA short-read The de-facto standard for whole-genome and exome alignment. Fast, accurate, and widely benchmarked.
Minimap2 Long-read / DNA / RNA Versatile aligner for PacBio, ONT, and short reads. Also supports splice-aware RNA mapping.
STAR RNA-seq (splice-aware) High-throughput splice-aware aligner for RNA-seq. Very fast but requires significant RAM (≥30 GB for human).
HISAT2 RNA-seq / DNA Memory-efficient splice-aware aligner using a graph FM index. Good balance of speed and RAM for RNA-seq.
Bowtie2 DNA short-read Fast, memory-efficient aligner. Common for ChIP-seq, ATAC-seq, and other assays where reads are short.
JapalitySplice RNA-seq (splice-aware) A sparse k-mer splice-aware RNA-seq aligner written in Rust, designed for resource-constrained environments and small teaching genomes. Also shipped as a mobile build for splice-site exploration.
JapalityAligner DNA short-read A memory-frugal short-read aligner (open-syncmer index; CPU or GPU paths). Useful for discussing what an index is doing. Production human genomes still usually go through BWA-MEM2 or equivalent.
Transcript Quantification

Pseudoalignment and lightweight mapping approaches that quantify transcript abundance without full genome alignment.

ToolDescription
Salmon Fast transcript quantification using selective alignment. Widely used for bulk RNA-seq DE analysis via tximeta/DESeq2.
Kallisto Near-optimal pseudoalignment for RNA-seq quantification. Extremely fast with a small memory footprint.
Variant Calling

Tools for identifying SNPs, indels, and structural variants from aligned reads.

ToolDescription
GATK Industry-standard variant calling toolkit (HaplotypeCaller, Mutect2, VQSR). Comprehensive but complex.
BCFtools Lightweight variant caller and VCF manipulation suite. Great for quick analyses and scripting.
DeepVariant CNN-based variant caller from Google. High accuracy, especially on whole-genome short-read data.
SAM/BAM Utilities

Essential utilities for manipulating, filtering, and summarizing alignment files.

ToolDescription
Samtools The standard tool for sorting, indexing, filtering, and inspecting SAM/BAM/CRAM files.
Picard Java-based BAM utilities for deduplication, metrics collection, and format conversion.
BEDTools Genomic interval arithmetic — intersect, merge, subtract intervals across BED/BAM/VCF files.
Differential Expression
ToolDescription
DESeq2 R/Bioconductor package for count-based DE using negative binomial models.
edgeR Alternative DE package using empirical Bayes estimation.
limma-voom Microarray-heritage DE with a voom transformation for RNA-seq count data.
Metagenomics & Taxonomy
ToolDescription
Kraken2 Ultra-fast k-mer-based taxonomic classification for metagenomic reads.
MetaPhlAn Marker-gene based metagenomic profiling at species level.
QIIME 2 Comprehensive microbiome analysis platform for amplicon and shotgun data.
MicroBioLens Custom-panel shotgun / 16S classifier (Rust). You choose the taxa; the tool classifies reads against that panel with cascade indexing. Good for teaching “database choice is the result” before you trust a mega-index.
Workflow Managers & Reproducibility

As pipelines grow in complexity, workflow managers help you orchestrate tools, handle dependencies, and ensure reproducibility.

ToolDescription
Nextflow DSL-based workflow manager with excellent container and cloud support. Powers nf-core community pipelines.
Snakemake Python-based workflow engine with automatic dependency resolution and cluster support.
CWL Common Workflow Language — a platform-agnostic specification for describing analysis workflows.
Browsers, primers, and figures

Each name below links to its official page, the same way FastQC and BWA do above. Use these when the lesson is “read this coordinate”, “explain this oligo”, or “choose an honest plot”.

ToolLessonDescription
IGV Genome browser The usual desktop genome browser for FASTA, BAM, VCF, and related tracks.
JBrowse Genome browser Embeddable / web genome browser used by many labs and genome projects.
UCSC Genome Browser Genome browser Public web browser for reference assemblies and community tracks.
Japality Genomics Viewer Genome browser On-device FASTA, GFF, BAM, VCF, and BigWig tracks for a small local teaching set.
Primer3 Primer design Standard desktop/server primer designer used in most molecular-biology workflows.
Primer-BLAST Primer design NCBI web tool that designs primers and checks them against a public database.
Japality Primer Primer design Length, GC, Tm, reverse complement, and ranked pairs from a pasted FASTA. Design only.
japality-primer Primer design CLI in silico PCR, IUPAC mismatch tolerance, multi-genome matrices, and FASTQ scanning.
pheatmap Choosing a plot Widely used R heatmap package for gene Ă— sample matrices.
ComplexHeatmap Choosing a plot Bioconductor heatmaps with annotations for publication figures.
UpSetR Choosing a plot R implementation of UpSet matrices for more than three sets.
Heatmap Creator Choosing a plot Small-CSV heatmaps for teaching captions before you move the same table into R.
Venn Diagram by Japality Choosing a plot Two- or three-set Venn diagrams with counts. Use UpSetR when a fourth set appears.
UpSet Plot Choosing a plot Mobile UpSet matrices for the same intersection exercise as UpSetR.
NCBI amino-acid table Choosing a plot Standard residue abbreviations and properties.
Amino Acids OTG Choosing a plot Flashcards and codon notes for the twenty residues.

Every tool name on this page links to an official project, paper, or product page. FastQLab, JapalitySplice, Japality Primer, Genomics Viewer, MicroBioLens, japality-primer, and the small plotters are published by Japality Limited, which also maintains this tutorial. They are listed in the same table format as FastQC, BWA, STAR, Primer3, and IGV.

How to choose a tool
Consider
  • Community & citations — widely used tools have more documentation and community support.
  • Hardware constraints — STAR needs ≥30 GB RAM for human; lighter tools exist for laptops/mobile.
  • Experiment type — DNA vs RNA vs metagenomics often dictates the pipeline.
  • Reproducibility — prefer tools with version-pinnable installs (Conda, containers).
Keep in mind
  • No single tool is best for every dataset and question.
  • Benchmarks on one species may not transfer to another.
  • Mobile/lightweight tools are great for teaching and previews, but production-scale work usually runs on servers.
  • Always validate outputs with independent QC checks.