Resources
Bioinformatics tools & glossary
109 plain-language entries covering the file formats, software, and statistical concepts you'll meet in a bioinformatics project. We name the tools we use openly—so if you see one in a methods section, you can look it up here.
109 terms, plainly defined
File Formats
The standard containers your data arrives in.
- FASTA
- Plain-text format storing nucleotide or protein sequences with a header line per record.
- FASTQ
- Raw sequencing reads plus a per-base quality score for each nucleotide.
- SAM / BAM
- Aligned reads against a reference; SAM is text, BAM is its compressed binary form.
- CRAM
- A reference-based compressed alignment format, smaller than BAM.
- VCF
- Variant Call Format: the standard record of variants (SNVs, indels) across samples.
- BED
- Simple tab-delimited genomic intervals, widely used for regions and peaks.
- GFF / GTF
- Annotation formats describing gene models and genomic features.
- mzML
- An open standard for raw mass-spectrometry data.
- AnnData / h5ad
- A container for single-cell matrices with cell and gene metadata.
- Newick
- A compact text notation for representing phylogenetic trees.
QC & Preprocessing
Establishing that the data is worth analysing.
- FastQC
- Generates per-sample quality reports from raw sequencing reads.
- MultiQC
- Aggregates QC reports from many samples and tools into one summary.
- fastp
- Fast all-in-one read trimming, filtering, and quality reporting.
- Trimmomatic
- Trims adapters and low-quality bases from Illumina reads.
- Cutadapt
- Removes adapter sequences and primers from high-throughput reads.
Alignment & Quantification
Placing reads on a reference, or counting them.
- BWA-MEM2
- Aligns DNA reads to a reference genome; a standard for WGS and WES.
- Bowtie2
- Fast gapped read aligner, common in ChIP-seq and ATAC-seq workflows.
- STAR
- Splice-aware aligner designed for RNA-seq reads spanning exon junctions.
- HISAT2
- Memory-efficient splice-aware aligner for transcriptomic data.
- minimap2
- Versatile aligner for long reads and whole-genome comparisons.
- Salmon
- Quantifies transcript abundance from RNA-seq without full alignment.
- kallisto
- Pseudoalignment-based transcript quantification, valued for speed.
- featureCounts
- Assigns aligned reads to genomic features to produce count matrices.
Assembly & Annotation
Building a genome when no reference exists.
- SPAdes
- Assembler widely used for bacterial and small-genome projects.
- Flye
- Long-read assembler for Nanopore and PacBio data.
- hifiasm
- Haplotype-resolved assembler built for PacBio HiFi reads.
- Unicycler
- Hybrid assembler combining short and long reads for bacterial genomes.
- QUAST
- Evaluates assembly quality with contiguity and correctness metrics.
- BUSCO
- Assesses assembly and annotation completeness using conserved orthologs.
- BRAKER
- Automated pipeline for structural gene annotation in new genomes.
Variant Calling & Annotation
Finding differences, then explaining them.
- GATK
- Broad Institute toolkit and best-practice workflows for variant discovery.
- bcftools
- Utilities for calling, filtering, and manipulating variants in VCF/BCF.
- DeepVariant
- Deep-learning germline variant caller producing highly accurate calls.
- Mutect2
- Somatic variant caller for tumour, with or without a matched normal.
- Strelka2
- Fast germline and somatic small-variant caller.
- Manta
- Detects structural variants and large indels from paired-end data.
- VEP
- Ensembl's Variant Effect Predictor: annotates consequence and impact.
- SnpEff
- Annotates and predicts the functional effects of genetic variants.
- AlphaMissense
- Model predicting the pathogenicity of missense variants.
Transcriptomics
From counts to differential expression and pathways.
- DESeq2
- Differential expression from count data using negative binomial models.
- edgeR
- Differential expression analysis for count data, with robust dispersion estimation.
- limma
- Linear models for expression data, widely used with the voom transformation.
- clusterProfiler
- Functional enrichment and pathway analysis of gene lists.
- GSEA
- Gene Set Enrichment Analysis: tests whether gene sets shift across a ranked list.
- rMATS
- Detects differential alternative splicing between conditions.
Single-Cell & Spatial
Resolving heterogeneity one cell at a time.
- Seurat
- R toolkit for single-cell QC, clustering, integration, and annotation.
- Scanpy
- Python equivalent for scalable single-cell analysis workflows.
- Cell Ranger
- 10x Genomics pipeline producing cell-by-gene matrices from raw reads.
- Harmony
- Batch-effect correction that integrates datasets in a shared embedding.
- UMAP
- Dimensionality reduction used to visualise cell populations in 2D.
- scVI
- Deep generative models for probabilistic single-cell analysis.
- Squidpy
- Analysis of spatial transcriptomics data and tissue neighbourhoods.
- CIBERSORTx
- Deconvolves bulk expression into constituent cell-type fractions.
Epigenomics
Regulation, chromatin, and methylation.
- MACS2
- Peak caller for ChIP-seq and ATAC-seq enrichment.
- deepTools
- Normalisation, coverage tracks, and visualisation for epigenomic data.
- ChromHMM
- Learns and annotates chromatin states from histone-mark combinations.
- Bismark
- Aligns and calls methylation from bisulfite sequencing data.
- methylKit
- Differential methylation analysis from sequencing or array data.
Metagenomics
Communities, not single organisms.
- Kraken2
- Fast taxonomic classification of metagenomic reads via k-mer matching.
- Bracken
- Re-estimates species abundance from Kraken2 classifications.
- MetaPhlAn
- Profiles microbial community composition using marker genes.
- HUMAnN
- Profiles the functional and pathway potential of a community.
- QIIME 2
- End-to-end platform for amplicon (16S/ITS) microbiome analysis.
- DADA2
- Infers exact amplicon sequence variants (ASVs) from amplicon reads.
Proteomics & Structure
Proteins, structures, and small molecules.
- MaxQuant
- Quantitative proteomics platform for mass-spectrometry data.
- DIA-NN
- Deep-learning-based analysis of data-independent acquisition proteomics.
- AlphaFold
- Predicts 3D protein structure from sequence with high accuracy.
- AutoDock Vina
- Molecular docking of small molecules into a protein binding site.
- GROMACS
- Molecular dynamics simulation of biomolecular systems.
- RDKit
- Open-source cheminformatics toolkit for handling molecular structures.
- PyMOL
- Molecular visualisation system for inspecting and rendering structures.
Phylogenetics & Population Genetics
Relatedness, ancestry, and evolution.
- MAFFT
- Multiple sequence alignment across many sequences.
- IQ-TREE
- Maximum-likelihood phylogenetic inference with model selection.
- RAxML
- Maximum-likelihood tree inference for large alignments.
- BEAST
- Bayesian phylogenetics and time-scaled phylodynamic inference.
- PLINK
- Whole-genome association and population-genetics analysis toolset.
- ADMIXTURE
- Estimates individual ancestry proportions from genotype data.
- ANGSD
- Population-genetic analysis from genotype likelihoods, robust at low coverage.
Workflow & Reproducibility
How a result stays a result.
- Nextflow
- Workflow language for portable, scalable, reproducible pipelines.
- Snakemake
- Python-based workflow manager using rule-driven dependency graphs.
- nf-core
- Community-curated collection of peer-reviewed Nextflow pipelines.
- Docker
- Packages software and dependencies into portable container images.
- Apptainer / Singularity
- Containers designed for shared HPC environments.
- Conda
- Environment and package manager for pinning software versions.
- Git
- Version control that records exactly how code and analysis changed.
Key Concepts
The vocabulary behind the tools—and the statistical ideas that decide whether a result holds up.
- Read
- A single sequence of bases produced by a sequencing instrument.
- Coverage / depth
- How many times, on average, each base is sequenced.
- Contig / scaffold
- A contiguous assembled sequence; scaffolds join contigs with gaps.
- Reference genome
- An assembled, annotated genome used as a coordinate system.
- Germline vs. somatic
- Inherited variants present in every cell, versus those acquired by a tissue.
- SNV / indel
- A single-base substitution, or a small insertion or deletion.
- Structural variant
- A large genomic rearrangement: deletion, duplication, inversion, or translocation.
- Allele frequency
- The proportion of chromosomes in a population carrying a given allele.
- Imputation
- Statistically inferring genotypes not directly measured, using a reference panel.
- Phasing
- Determining which variants sit together on the same parental chromosome.
- Batch effect
- Systematic technical variation that can masquerade as biological signal.
- Normalisation
- Adjusting measurements so samples can be compared fairly.
- TPM / CPM
- Expression units normalised for sequencing depth (and, for TPM, gene length).
- log2 fold change
- The log-scaled ratio of expression between two conditions.
- p-value
- The probability of observing a result at least as extreme if the null hypothesis were true.
- Multiple testing
- Testing thousands of hypotheses inflates false positives unless corrected.
- FDR
- False Discovery Rate: the expected proportion of false positives among significant results.
- Power
- The probability a study detects a true effect; low power means real effects are missed.
- PCA
- Projects high-dimensional data onto axes capturing the most variance.
- Overfitting
- A model that learns noise in training data and fails to generalise.
- Cross-validation
- Holding out data to estimate how a model performs on unseen samples.
- GWAS
- Tests common variants genome-wide for association with a trait.
- eQTL
- A variant associated with the expression level of a gene.
- Pathway enrichment
- Testing whether a gene list is over-represented in known biological pathways.
Tool names change; the reasoning doesn't. A method is only appropriate for a particular question, data type, and sample size—no entry here should be read as a recommendation for your project. If you're deciding between approaches, that's a conversation worth having before you commit compute to it.
Related
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