Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. These genome assemblies may not be equivalent to assemblies for the same species in other genome browsers.The NCBI Assembly database ( provides stable accessioning and data tracking for genome assembly data. A number of genome assemblies in Ensembl were annotated prior to the Genome Browser Agreement. Region in detail) to the equivalent region in NCBI and UCSC. We provide links on our Location pages (eg. To know whether the assembly that you're viewing in Ensembl is the same as the assembly in another genome browser, compare the Genome Collections Accession found on the species home page. This accession identifies the genome assembly version for a species and the version is incremented each time any change is made to the sequence data. It has been in place for a number of years, and it establishes the minimum requirements for public display of genome data by the Ensembl, NCBI and UCSC browsers/annotation groups.įor species that have been annotated since the Genome Browser agreement, all genome assemblies have been assigned a unique Genome Collections Accession (GCA). The Genome Browser Agreement guarantees consistency between major projects. This allows users to attach and view their files in any genome browser. BAM, it is important to have consistent genomic coordinates across the genome browsers. With the increasing use of big data file formats eg. Ensembl, NCBI and UCSC make a joint decision on which assembly to annotate, in consultation with the species community where possible.įind out more about how genome assemblies are put together and how we use them in Ensembl: For some species, more than one genome assembly has been produced. We select species to annotate on a case-by-case basis according to a number of factors such as: phylogenetic position, assembly quality, model organism, availability of species-specific sequence data (eg. This means that any region may contain alleles that are rare or even private to that individual.Įnsembl does not produce genome assemblies, instead we provide annotation on genome assemblies that have been deposited into the INSDC (GenBank, ENA, DDBJ) and are publicly available. Some assemblies are made up of sequences from multiple individuals (such as human), while some from a single individual (such as cat), however each section of sequence comes from one individual. This always creates some gaps and errors. Because we are not able to sequence along the complete length of a chromosome, each chromosome assembly is made up of short stretches of sequenced DNA pasted together. A genome assembly is a computational representation of a genome sequence.
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