Life & Health Sciences
Genomics and bioinformatics research
Genomics and bioinformatics research runs on shared sequence archives and on the rules for putting data into them. The International Nucleotide Sequence Database Collaboration links NCBI in the US, the European Nucleotide Archive at EMBL-EBI and DDBJ in Japan, which together archive nucleotide data from raw reads to assembled and annotated sequences. Raw reads go to the Sequence Read Archive, expression studies to NCBI's Gene Expression Omnibus under the MIAME reporting standard, and human genotype and phenotype data to dbGaP or, in Europe, the European Genome-phenome Archive. Both hold controlled-access human data: researchers apply for access, and at EGA the decision belongs to the data access organisation, not the archive. For NIH-funded human genomic data, a dbGaP submission needs IRB review and an institutional certification, participants must be told their data will be shared, and only coded data are accepted. GA4GH, formed in 2013, maintains the field's technical standards, among them the SAM/BAM, CRAM and VCF formats, the htsget and Beacon APIs, Passports and the Data Use Ontology. Data should meet the FAIR principles published in Scientific Data in 2016. Analysis runs on open tools such as Bioconductor, R packages released twice a year, and Galaxy, a web platform with free public servers. NHGRI is the NIH institute that funds genomics, and ISCB is the field's international society.
New to the field? What is Genomics & Bioinformatics? →
Reviewed 5 November 2026 by CASRAI Editorial Board
- INSDC home(read 5 November 2026)
- Wikipedia: European Nucleotide Archive(read 5 November 2026)
- Wikipedia: Sequence Read Archive(read 5 November 2026)
- Wikipedia: Gene Expression Omnibus(read 5 November 2026)
- dbGaP home(read 5 November 2026)
- Wikipedia: European Genome-phenome Archive(read 5 November 2026)
- Ohio State Office of Research: Submission of Data to dbGaP and Genomic Data Sharing(read 5 November 2026)
- GA4GH: About us(read 5 November 2026)
- GA4GH: Our products(read 5 November 2026)
- GO FAIR Foundation: FAIR principles(read 5 November 2026)
- Bioconductor: About(read 5 November 2026)
- Galaxy Project(read 5 November 2026)
- Wikipedia: National Human Genome Research Institute(read 5 November 2026)
- ISCB: About(read 5 November 2026)
- Nucleic Acids Research: About(read 5 November 2026)
- Bioinformatics: About(read 5 November 2026)
Field at a glance
Archives, facilities and data
- INSDC
- Collaboration of NCBI, EMBL-EBI (ENA) and DDBJ that archives nucleotide sequence data from raw reads to assembled and annotated sequences.Website ↗
- European Nucleotide Archive (ENA)
- EMBL-EBI's open archive of annotated DNA and RNA sequences and sequencing metadata; an INSDC member that exchanges submissions daily with DDBJ and GenBank.Website ↗
- Sequence Read Archive (SRA)
- INSDC repository for raw sequencing reads, established by NCBI in 2007; BAM is the preferred submission format, and the SRA Toolkit converts to FASTQ.Website ↗ · Our guide →
- Gene Expression Omnibus (GEO)
- NCBI database of microarray and RNA-seq expression and methylation data, organised as GSE series, GSM samples and GPL platforms; submissions follow MIAME.Website ↗ · Our guide →
- dbGaP
- NCBI archive for human genotype and phenotype studies; public data download directly, controlled data need an Authorized Access request.Website ↗ · Our guide →
- European Genome-phenome Archive (EGA)
- Controlled-access archive for identifiable human genetic and phenotypic data, run by EMBL-EBI and CRG; the data access organisation decides who gets access.Website ↗
- Bioconductor
- Open-source project, started in 2001, that distributes R packages for analysing biological assay data, with a new release twice a year.Website ↗
- Galaxy
- Open-source web platform for running tools and workflows without the command line, tracking every step; free public servers include usegalaxy.org and usegalaxy.eu.Website ↗
Standards and formats
- GA4GH standards
- Global Alliance for Genomics and Health products include SAM/BAM, CRAM, VCF, htsget, Beacon, DRS, Passports and the Data Use Ontology.Website ↗ · Our guide →
- FAIR principles
- Findable, Accessible, Interoperable, Reusable: data principles published in Scientific Data in 2016, stressing machine-readable metadata.Website ↗ · Our guide →
Funders and programmes
- National Human Genome Research Institute (NHGRI)
- NIH institute, elevated to full institute status in 1997, that funds genomics research through grants; in 1990 it set aside 5% of its budget for ethical, legal and social research.Website ↗
- NIH Genomic Data Sharing Policy
- Covers large-scale human genomic data such as GWAS; submissions to dbGaP need IRB review, institutional certification and coded data only.Website ↗ · Our guide →
Journals
- Nucleic Acids Research
- Nucleic acids journal whose first issue each year is devoted to biological databases and a July issue to web server tools.Website ↗
- Bioinformatics
- Oxford University Press journal shown with the ISCB logo, focused on genome bioinformatics and computational biology; fully open access since January 2023.Website ↗
Societies
- International Society for Computational Biology (ISCB)
- Non-profit society founded in 1997 for computational biology and bioinformatics, serving over 4,000 researchers and practitioners worldwide.Website ↗
54 pages across 9 topic areas
Research Tools & Software
- ACMG/AMP Variant Classification Criteria for Research Variant Calls
How the ACMG/AMP five-tier framework — Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign — classifies a called variant using weighted evidence…
- BAM Index (.bai) Files: Why You Need One and How to Build It
Why a BAM file needs a coordinate-sorted .bai index for fast region queries, how to build one with samtools index, and what breaks when the index is m…
- Choosing a Reference Genome File: Analysis Sets, Alt Contigs, and Decoys
You've picked a genome build — now which specific file do you download? A plain-English guide to analysis sets, alt contigs, and decoy sequences, and…
- De Novo Genome Assembly: Choosing an Assembler
How to choose a de novo genome assembler by read type — short-read (SPAdes), long-read (Flye, Canu), and PacBio HiFi (hifiasm) — plus BUSCO/N50 qualit…
- DeepVariant vs GATK HaplotypeCaller: Accuracy, Cost, and When to SwitchComparison
DeepVariant's deep-learning pileup-image classifier vs GATK HaplotypeCaller's statistical local-reassembly caller: benchmark accuracy, GPU/CPU cost tr…
- FASTQ Format Explained: Structure, Quality Encoding, and Header Fields
The FASTQ file format explained: the four-line record structure, how Phred+33/Phred+64 quality scores are ASCII-encoded, what a header line encodes, a…
- GRCh38 vs hg38 vs b37: The Naming, Not the CoordinatesComparison
GRCh38 and hg38 are the same human reference-genome assembly under two names; b37 is the prior assembly they replaced. The real trap is the 'chr' pref…
- MAFFT vs MUSCLE vs Clustal Omega vs T-Coffee: Multiple Sequence Alignment Tools ComparedComparison
A technical comparison of MAFFT, MUSCLE, Clustal Omega and T-Coffee for multiple sequence alignment: algorithmic approach, scalability and accuracy tr…
- N50 in Genome Assembly: How It's Calculated and Why It's Not Enough Alone
N50 is the standard genome-assembly contiguity statistic — the contig length at which half the assembly's total length is contained in contigs that lo…
- Reading a VCF: The Header, INFO/FORMAT Fields, and the Columns People Misread
How VCF meta-information headers, the 8 fixed columns, semicolon-delimited INFO annotations, and per-sample FORMAT/genotype columns fit together — inc…
- Volcano Plots in RNA-seq: How to Build and Correctly Read Differential Expression Results
What a volcano plot actually plots, why using raw p-values instead of FDR-adjusted p-values is a serious and common error, how to choose defensible fo…
- What Is a BAM File? Format, Structure, and Tools
A BAM file is the compressed, indexed binary counterpart to a SAM alignment file. What it is, how it is structured, and the samtools commands used to…
- What Is a LIMS? Laboratory Information Management System Explained
A Laboratory Information Management System (LIMS) tracks lab samples, workflows, and results with a full audit trail. This guide explains what a LIMS…
- What Is an Open Reading Frame? How to Find One With NCBI ORFfinder
An open reading frame is a stretch of DNA with no stop codon. Learn the definition and how to find ORFs with NCBI ORFfinder, step by step.…
Research Data Management
- dbGaP: Submission and Controlled-Access Data Requests
How dbGaP submission and controlled-access data requests actually work: study registration and file submission for data-generating investigators, and…
- EGA (European Genome-Phenome Archive): The EU's Controlled-Access Counterpart to dbGaP
The European Genome-phenome Archive (EGA) is the EU's controlled-access repository for human genomic, phenotypic, and clinical research data, jointly…
- Gene Expression Omnibus (GEO): NCBI's Repository, MIAME/MINSEQE, and Accession Numbers
GEO is NCBI's public repository for gene-expression data, built around the MIAME/MINSEQE minimum-information standards and a GSE/GSM/GPL/GDS accession…
- H3Africa's Data and Biospecimen Access Committee (DBAC): A Governance Model for African Genomic Research
How H3Africa's Data and Biospecimen Access Committee (DBAC) governs access to African genomic data and biospecimens collected under broad consent, inc…
- InterPro: Protein Families, Member Databases, InterProScan and Citation
InterPro classifies protein sequences into families and domains using member databases such as Pfam and SMART. Access routes, InterProScan and citatio…
- NIH Genomic Data Sharing Policy and Institutional Certification
Who signs the NIH Institutional Certification, what it attests, and how it gates dbGaP genomic data submission — with the full step-by-step workflow f…
- Protein Data Bank (PDB): Archiving and Reusing Macromolecular Structure Data
How the Protein Data Bank archives experimentally determined 3D macromolecular structures, wwPDB governance, deposition mandates, formats, and reuse i…
- ProteomeXchange: The Proteomics Repository Consortium and PXD Accession Numbers
ProteomeXchange is the international consortium that coordinates the world's mass spectrometry proteomics repositories under a single PXD accession-nu…
- Snakemake vs Nextflow for Reproducible WorkflowsComparison
Snakemake and Nextflow compared for reproducible computational research pipelines: workflow language, execution model, containers, cluster/cloud suppo…
- Submitting Sequence Data to NCBI SRA
A step-by-step guide to depositing sequencing reads in NCBI SRA: how BioProject, BioSample, and SRA run accessions relate, when to route data to dbGaP…
- UK Biobank Data Access: Tiers, Cost, and How to Apply
UK Biobank's 500,000-participant cohort is one of the most heavily used population-health resources in research -- but access requires a scoped applic…
- UniProt: The Protein Sequence and Functional Annotation Knowledgebase
UniProt is the primary knowledgebase for protein sequence and functional annotation data, curated by a consortium of EMBL-EBI, SIB, and PIR. This guid…
Laboratory Operations & Safety
- ATAC-seq: Tagmentation, Quality Control and Failure Modes
ATAC-seq maps open chromatin by Tn5 tagmentation. The practical difficulty is that 20-80% of reads can be mitochondrial, and library quality is decide…
- ChIP-seq: Antibody Choice, Controls and Quality Metrics
ChIP-seq maps where a protein binds the genome. The antibody decides data quality, input control is mandatory, and only a spike-in lets you compare gl…
- Differential Gene Expression Analysis: How to Model, Test and Read the Result
A practitioner's guide to differential gene expression analysis: why the model needs raw counts, how dispersion and fold-change shrinkage work, how to…
- DNA Purification: Methods and How Each Works
DNA purification methods compared: silica columns, magnetic beads, precipitation and organic extraction, with vendor yield figures by sample type.…
- Index Hopping: How Reads End Up in the Wrong Sample, and How to Detect It
Index hopping is a low-level cross-contamination artifact in multiplexed NGS runs, most pronounced on patterned flow cells with ExAmp chemistry. Here'…
- JASPAR: Transcription Factor Binding Profile Database Explained
JASPAR is an open-access database of curated transcription factor binding profiles. See its collections, access routes and how to cite the release.…
- Leiden Clustering for Single-Cell Data: How the Algorithm Works and How to Tune It
Leiden partitions a k-nearest-neighbour graph in three phases and, unlike Louvain, guarantees connected communities. But it returns clusters from homo…
- RNA-seq: Experimental Design Through Analysis
A practical guide to planning an RNA-seq experiment: biological replicates, batch effects, the replicate-versus-depth trade-off, library prep choices,…
- Spatial Proteomics: Methods for Mapping Proteins to Tissue Location
A working comparison of spatial proteomics methods for mapping proteins to tissue location — targeted multiplexed imaging versus discovery mass…
Research Methods & Statistics
- Genetics vs Epigenetics: What Is the Difference?Comparison
Genetics studies the DNA sequence and how it is inherited; epigenetics studies the chemical marks on DNA and its packaging proteins that change how ge…
- Genome-Wide Significance Thresholds in GWAS: Why p < 5×10⁻⁸?
The conventional p < 5×10⁻⁸ threshold GWAS uses for genome-wide significance, where the number comes from, the suggestive-significance threshold, a…
- How to Read a Phylogenetic Tree: Nodes, Branch Lengths and Bootstrap Values
Nodes, branch lengths, tip order and the numbers on the branches (bootstrap values vs Bayesian posterior probabilities) explained with a worked interp…
- Linkage Disequilibrium: D, D′ and r² Explained with a Worked Example
What linkage disequilibrium is, how D, D′ and r² are calculated and read, with a worked example and PLINK, LDlink, R and Python code.…
- What Is Epigenetics?
Epigenetics is the study of chemical marks on DNA and its packaging proteins that regulate gene activity without changing the DNA sequence. Mechanisms…
- What Is Proteomics? Research Areas, Funding, and Career Paths
What proteomics studies, its major subfields, who funds the research (NIH, NSF, CZI), core lab methods (mass spectrometry), and typical career and PhD…
- What Is Systems Biology? Research Areas, Funding, and Career Paths
Systems biology studies biological organisms as integrated networks of interacting components, combining measurement, mathematical modelling and compu…
Laboratory Equipment & Instrumentation
- Mass Spectrometry Proteomics: Choosing DDA or DIA, Sample Prep, and Run QC
A decision guide to bottom-up mass spectrometry proteomics: choosing between DDA and DIA acquisition, the digestion, cleanup and fractionation choices…
- Pipette Tips: Selection Guide by Application
How to choose pipette tips by application: filter/barrier vs. standard, low-retention vs. standard, sterile vs. autoclavable, and rack vs. bulk format…
- Protein Identification by Mass Spectrometry: Workflow and Database Search
How bottom-up mass spectrometry identifies proteins, and the database-search parameter choices — enzyme specificity, missed cleavages, fixed/variable…
- qPCR Melt Curve Analysis: Reading Peaks, Primer Dimers and the Confirmatory Check
A diagnostic reading of the qPCR dissociation curve: which peak shapes mean primer dimer, which mean non-specific amplicon, why there is no universal…
- RNA Integrity Number (RIN): How It Is Computed and How to Read a Trace
What the RIN algorithm actually computes (nine electropherogram regions and a neural network trained on 1,208 samples, not the 28S:18S ratio it replac…
Scholarly Publishing
- Biopython: Python Tools for Bioinformatics
Biopython is an open-source suite of Python libraries providing standardized parsers, data models, and database interfaces for computational biology r…
- NCBI Gene: RefSeq, Gene IDs & Search
A comprehensive guide to NCBI Gene, explaining stable GeneIDs, curated RefSeq transcript models, genomic coordinates, Datasets export, and researcher…
- NCBI Taxonomy: TaxIDs, Tree Structure & Guide
A comprehensive guide to the NCBI Taxonomy database, explaining TaxIDs, phylogenetic tree structure, 8 taxonomic categories, Datasets export, and bioi…
- STROBE-MR: Reporting Mendelian Randomisation Studies
STROBE-MR is the 20-item reporting-guideline extension to STROBE for Mendelian randomisation studies — covering genetic instrument selection, the thre…
Clinical Research Administration
- Biobank Specimen Consent Models: Broad, Tiered, and Dynamic Consent Compared
A comparison of the three main biobank consent architectures — broad, tiered, and dynamic consent — and how each aligns with ISO 20387 biobank accredi…
CRediT & Authorship
- Genomics Megaconsortium Authorship: How UK Biobank and Large Sequencing Papers Credit Hundreds of Scientists
How UK Biobank-scale whole-genome-sequencing papers assign and list credit across hundreds of scientists: a single group-name byline, tiered leadershi…
Research Integrity & Compliance
- CRISPR Ethics: Germline Editing, He Jiankui, and Oversight
The bioethics debate over CRISPR gene editing: the somatic-vs-germline distinction, the 2018 He Jiankui case and its legal outcome, international mora…
Key terms
- 1000 Genomes Project
- All of Us Research Program
- BioSample
- ClinVar
- ENCODE (Encyclopedia of DNA Elements)
- GA4GH (Global Alliance for Genomics and Health)
- gnomAD (Genome Aggregation Database)
- Human Cell Atlas (HCA)
- KEGG (Kyoto Encyclopedia of Genes and Genomes)
- NIH Genomic Data Sharing (GDS) Policy
- PharmGKB (Now ClinPGx): The Pharmacogenomics Knowledgebase
- Sequence Read Archive (SRA)
- STRING (Protein-Protein Interaction Networks)
- Workflow Language (CWL/WDL)
