Sequencing platforms, technologies and providers
Official pages from major sequencing-technology providers and comparison resources useful for planning NGS experiments.
Illumina
Official Illumina site for sequencing instruments, SBS chemistry, library preparation, panels and NGS application resources.
https://www.illumina.comIllumina sequencing-platform comparison tool
Practical tool for comparing Illumina instruments by output, read length, run time and application suitability.
https://emea.illumina.com/systems/sequencing-platforms/comparison-tool.htmlThermo Fisher Scientific
Official site for Ion Torrent sequencing systems, Oncomine panels, sample preparation and molecular-biology reagents.
https://www.thermofisher.comBGI
Large international genomics organisation offering sequencing, multi-omics and related life-science services.
https://www.bgi.comPacBio
Official site for PacBio long-read HiFi sequencing instruments and applications including genomes, isoforms, methylation and structural variants.
https://www.pacb.comOxford Nanopore Technologies
Official site for nanopore sequencing instruments, real-time sequencing, long-read applications and direct RNA/DNA sequencing.
https://nanoporetech.comMGI Tech
Official site for DNBSEQ sequencing platforms, automation systems and sequencing workflow solutions.
https://en.mgi-tech.com/Element Biosciences
Official site for AVITI sequencing systems and avidity-based short-read sequencing technology.
https://www.elementbiosciences.com/Ultima Genomics
Official site for ultra-high-throughput short-read sequencing platforms designed for large-scale genomics.
https://www.ultimagenomics.com/Core bioinformatics tools and workflow frameworks
Widely used software, workflow engines and QC tools for reproducible NGS analysis.
GATK
Broad Institute toolkit for variant discovery, germline and somatic variant calling, CNV workflows and best-practice documentation.
https://gatk.broadinstitute.org/Novoalign / Novocraft
Commercial short-read alignment tools historically used for accurate mapping of NGS reads.
http://novocraft.com/Real Time Genomics RTG Tools
Command-line utilities for variant comparison, VCF manipulation and benchmarking tasks.
https://www.realtimegenomics.com/news/rtg-core-3-9-rtg-tools-3-9-releasedFastQC
Standard quality-control tool for assessing raw FASTQ sequencing reads.
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/MultiQC
Aggregates reports from FastQC, aligners, quantifiers and many other tools into a single project-level QC report.
https://multiqc.info/SAMtools / HTSlib / BCFtools
Essential toolkit for SAM/BAM/CRAM and VCF/BCF processing, indexing, filtering and statistics.
https://www.htslib.org/BEDTools
Powerful utilities for genomic-interval operations such as overlaps, intersections, coverage and sequence extraction.
https://bedtools.readthedocs.io/IGV
Interactive genome browser for visual inspection of BAM, CRAM, VCF, BED, bigWig and other genomic data tracks.
https://igv.org/Nextflow
Workflow language and execution engine for scalable, reproducible bioinformatics pipelines across local, HPC and cloud environments.
https://www.nextflow.io/nf-core
Community collection of curated, tested Nextflow pipelines for RNA-seq, variant calling, methylation, single-cell and many other omics workflows.
https://nf-co.re/Snakemake
Workflow-management system for reproducible and portable data-analysis pipelines.
https://snakemake.readthedocs.io/Galaxy
Web-based platform for accessible, reproducible bioinformatics analyses without requiring extensive command-line work.
https://usegalaxy.org/Bioconductor
Large R-based ecosystem for statistical analysis, visualization and interpretation of genomic and transcriptomic data.
https://www.bioconductor.org/Read alignment, transcriptomics and quantification
Commonly used aligners, transcript quantifiers and reference resources for RNA-seq and DNA-seq workflows.
BWA
Widely used aligner for short DNA sequencing reads, especially WGS, WES and targeted DNA-seq workflows.
https://bio-bwa.sourceforge.net/Bowtie2
Fast and memory-efficient aligner for short reads, useful in many targeted, metagenomic and general alignment workflows.
https://bowtie-bio.sourceforge.net/bowtie2/HISAT2
Splice-aware aligner often used for RNA-seq analysis, especially with graph-based genome indexes.
https://daehwankimlab.github.io/hisat2/STAR
High-performance splice-aware aligner widely used for bulk and single-cell RNA-seq data.
https://github.com/alexdobin/STARSalmon
Fast transcript-level quantification tool for RNA-seq using lightweight mapping or alignment-based modes.
https://salmon.readthedocs.io/Kallisto
Efficient RNA-seq transcript quantification tool based on pseudoalignment.
https://pachterlab.github.io/kallisto/GENCODE
High-quality human and mouse gene annotation resource commonly used for RNA-seq and genome annotation.
https://www.gencodegenes.org/NCBI RefSeq
Curated reference sequence database for genomes, transcripts and proteins.
https://www.ncbi.nlm.nih.gov/refseq/SRA Toolkit
NCBI tools for downloading and converting public Sequence Read Archive data.
https://github.com/ncbi/sra-toolsHuman genetic variation, clinical genetics and population databases
Resources for population allele frequencies, clinical variant interpretation, disease association and variant databases.
Human Genome Project results
NHGRI overview of the Human Genome Project results and their scientific impact.
https://www.genome.gov/human-genome-project/results1000 Genomes Project
Population-scale catalogue of human genetic variation across multiple global populations.
https://www.internationalgenome.org/gnomAD
Large population allele-frequency resource essential for filtering and interpreting human genetic variants.
https://gnomad.broadinstitute.org/UK Biobank genetic browser
Search interface for genetic and phenotypic data resources related to UK Biobank.
http://biobank.ctsu.ox.ac.uk/crystal/gsearch.cgiClinVar
Public archive of relationships among human genetic variants and clinical significance.
https://www.ncbi.nlm.nih.gov/clinvar/MedGen
NCBI resource for medical genetics concepts, phenotypes, disorders and terminology mappings.
https://www.ncbi.nlm.nih.gov/medgen/GWAS Catalog
Curated catalogue of published genome-wide association studies and trait-associated variants.
https://www.ebi.ac.uk/gwas/GWASdb
Database of variants identified from genome-wide association studies and related annotations.
http://jjwanglab.org/gwasdbEuropean Variation Archive
EMBL-EBI archive for genetic variation data across species, including variant submissions and study metadata.
https://www.ebi.ac.uk/evaHuman Variome Project
International initiative focused on collection, curation and sharing of human genetic variation information.
https://www.humanvariomeproject.org/ClinGen
Clinical Genome Resource for gene-disease validity, dosage sensitivity and expert variant curation.
https://www.clinicalgenome.org/dbSNP
NCBI database of short genetic variants, including SNPs and small insertions/deletions.
https://www.ncbi.nlm.nih.gov/snp/dbVar
NCBI archive of human and non-human structural variation data.
https://www.ncbi.nlm.nih.gov/dbvar/dbGaP
Controlled-access NIH database for genotype and phenotype studies.
https://www.ncbi.nlm.nih.gov/gap/PharmGKB
Pharmacogenomics knowledgebase linking genetic variation to drug response, dosing and clinical annotations.
https://www.pharmgkb.org/Gene-disease, phenotype and rare-disease resources
Resources for linking genes, variants, phenotypes, syndromes and disease mechanisms.
DisGeNET
Platform integrating gene-disease and variant-disease associations from curated and text-mined sources.
https://www.disgenet.org/Monarch Initiative
Integrated resource connecting genes, genotypes, diseases and phenotypes across species.
https://monarchinitiative.org/EDGAR gene-disease database
Gene-disease association database useful for exploring disease-linked genes and literature-derived relationships.
http://edgar.biocomp.unibo.it/gene_disease_db/MalaCards
Integrated human disease database combining gene, phenotype, pathway and literature information.
https://www.malacards.org/Orphanet
Authoritative portal for rare diseases, orphan drugs, disease classifications and expert resources.
https://www.orpha.net/Geno2MP
Genotype-to-Mendelian-phenotype browser useful for exploring rare variant and phenotype relationships.
https://geno2mp.gs.washington.edu/Geno2MPOMIM
Comprehensive catalogue of human genes and genetic disorders with curated Mendelian disease information.
https://www.omim.org/Leiden Open Variation Database / LSDB list
List of locus-specific databases and variant resources historically associated with LOVD-style curation.
https://grenada.lumc.nl/LSDB_list/lsdbsHuman Phenotype Ontology
Standardized vocabulary and resource for describing phenotypic abnormalities in human disease.
https://hpo.jax.org/GeneReviews
Expert-authored clinical summaries for inherited conditions, including diagnosis, management and genetic counselling.
https://www.ncbi.nlm.nih.gov/books/NBK1116/Cancer genomics and precision-oncology resources
Curated cancer-genomics and oncology-variant resources useful for tumour profiling, driver interpretation and research.
COSMIC
Catalogue of somatic mutations in cancer, including cancer gene curation and mutation frequency information.
https://www.cosmickb.org/OncoKB
Precision-oncology knowledgebase for biological and clinical interpretation of cancer variants.
https://www.oncokb.org/CIViC
Open, evidence-based resource for clinical interpretation of variants in cancer.
https://civicdb.org/cBioPortal
Interactive portal for exploring cancer genomics datasets, mutations, copy-number changes, expression and clinical associations.
https://www.cbioportal.org/NCI Genomic Data Commons
NCI portal for accessing and analysing harmonized cancer genomics data, including TCGA and TARGET datasets.
https://portal.gdc.cancer.gov/ICGC ARGO
International cancer genome initiative focused on clinically linked cancer genome data.
https://www.icgc-argo.org/Genome browsers, annotation and reference resources
Core portals for genome annotation, coordinates, sequence retrieval, visual inspection and variant annotation.
Ensembl
Genome browser and annotation platform for vertebrate genomes, gene models, comparative genomics and variation.
http://www.ensembl.orgUCSC Genome Browser
Genome browser for visualizing genes, variants, regulatory tracks, alignments and custom genomic annotations.
https://genome.ucsc.edu/NCBI Remap / Genome Remapping Service
NCBI tool for converting annotation coordinates between genome assemblies.
https://www.ncbi.nlm.nih.gov/variation/tools/get-rm/Ensembl Variant Effect Predictor
Widely used tool for annotating genetic variants with predicted molecular consequences and database information.
https://www.ensembl.org/info/docs/tools/vep/index.htmlNCBI Genome Data Viewer
NCBI browser for viewing genome assemblies, genes, variation tracks and annotations.
https://www.ncbi.nlm.nih.gov/genome/gdv/UCSC LiftOver
Tool for converting genomic coordinates between assemblies using UCSC chain files.
https://genome.ucsc.edu/cgi-bin/hgLiftOverPathways, proteins and functional interpretation
Useful resources for gene-function interpretation, pathway enrichment and biological-network analysis.
UniProt
Comprehensive protein sequence and functional annotation resource.
https://www.uniprot.org/Gene Ontology
Structured vocabulary for gene-product functions, biological processes and cellular components.
http://geneontology.org/Reactome
Curated pathway database for interpreting gene lists, pathways and biological processes.
https://reactome.org/KEGG
Database suite for pathways, genomes, enzymes, compounds and systems biology interpretation.
https://www.genome.jp/kegg/STRING
Protein-protein interaction and functional-association network resource.
https://string-db.org/MSigDB / GSEA
Gene-set collections and enrichment-analysis resources for transcriptomic and pathway interpretation.
https://www.gsea-msigdb.org/gsea/msigdb/Public datasets, cloud platforms and reproducible analysis environments
Platforms for public sequencing data, large-scale analysis, collaboration and cloud-based bioinformatics.
Terra
Cloud-based biomedical research platform for scalable workflows, data sharing and collaborative analysis.
https://terra.bio/Seven Bridges
Cloud bioinformatics platform for scalable NGS workflows, data management and regulated analysis environments.
https://www.sevenbridges.com/NCBI Sequence Read Archive
Large public archive of raw high-throughput sequencing data from published and submitted studies.
https://www.ncbi.nlm.nih.gov/sraEuropean Nucleotide Archive
European archive for nucleotide sequences, raw reads, assemblies and functional annotation.
https://www.ebi.ac.uk/ena/browser/homeNCBI GEO
Public repository for gene-expression and functional-genomics datasets, including many RNA-seq studies.
https://www.ncbi.nlm.nih.gov/geo/EMBL-EBI BioStudies
Repository for biological studies, supplementary files and datasets linked to publications.
https://www.ebi.ac.uk/biostudies/AnVIL
NHGRI genomic data science analysis, visualization and informatics platform built on cloud infrastructure.
https://anvilproject.org/NCBI Datasets
NCBI portal and tools for downloading genomes, genes, orthologs, taxonomy and related biological datasets.
https://www.ncbi.nlm.nih.gov/datasets/