#reference-genome

Reference genome assemblies as an API — powered by NCBI Assembly, the registry of genome builds for organisms across the tree of life. Search assemblies by organism (or free text) and look up any assembly's metadata: its accession (GCF_… RefSeq or GCA_… GenBank), name (e.g. GRCh38.p14), organism and taxon id, assembly level (complete genome, chromosome, scaffold or contig), contiguity statistics (contig and scaffold N50), sequencing coverage, RefSeq category, UCSC and Ensembl names, the submitting organization, release date and FTP download paths. From the human reference genome to any sequenced microbe, plant or animal, it turns the genome-assembly registry into a clean search-and-fetch API. A genome-assembly registry — distinct from sequence (ENA), genome annotation (Ensembl), variant (ClinVar, dbVar) and gene-expression (GEO) databases. Open data from NCBI Assembly (public domain).

api.oanor.com/genomes-api

The UCSC Genome Browser as an API — reference genome data for hundreds of species, from the renowned UCSC Genome Browser at UC Santa Cruz. /v1/genomes lists the 220+ genome assemblies UCSC hosts, each with its assembly id (such as hg38 for human, mm39 for mouse, danRer11 for zebrafish), organism, description and data source. /v1/chromosomes?genome=hg38 returns an assembly's chromosomes and sequences with their sizes in base pairs, largest first. /v1/sequence?genome=hg38&chrom=chrM&start=0&end=100 retrieves the raw DNA sequence of any genomic region (0-based start, half-open end; regions are capped at 100,000 bases per call). Assembly ids come from /v1/genomes and chromosome names look like chr1, chrX or chrM. Ideal for bioinformatics pipelines, genome-visualisation and primer-design tools, region and sequence lookups, comparative genomics and teaching. Data from the UCSC Genome Browser (free for academic, non-profit and personal use). This is the genome browser's assemblies and raw reference sequence — distinct from gene-annotation and protein-sequence databases such as Ensembl, UniProt and ENA.

api.oanor.com/ucsc-api