![]() ![]() In addition, the database calculates numerous statistics from the sequences in each assembly so that users can evaluate different assemblies by comparing their statistics and it also tracks assembly updates so that users can see the history of previous versions for an assembly. This enables the Assembly database to report the assembly structure and to provide mappings between names, synonyms and identifiers for assemblies, chromosomes or scaffolds. The Assembly database stores the names and identifiers for the sequences in each genome assembly and records the organization of the component sequences into scaffolds and chromosomes. The Assembly database is the first database to provide a unique, unambiguous and stable identifier for the set of sequences that comprise a specific version of a genome assembly. We have designed and built the Assembly database to provide the means by which the precise collection of sequences that constitute an assembly can be unambiguously tied together. If data from different sources are reported on the same set of sequences, these data are guaranteed to be in the same coordinate system and can be directly compared or integrated to produce a more complete view of the biological ramifications of the data. Knowing the exact set of sequences used to define coordinate systems is a prerequisite for making full use of this wealth of genomics data. We are in a period of extraordinary growth in genomics data, with new sequencing technologies ( 1) enabling the mass production of genome sequences, as well as the gene expression, variation discovery and epigenomic data vital to interpret those genome sequences. The multiple assembly versions for an organism need to be clearly identified, differentiated and tracked in a way that allows researchers to unambiguously refer to the set of sequences that comprise a particular version of a genome assembly. ![]() Multiple sequencing groups may produce different genome assemblies for the same organism and any one group may release different versions of an assembly as they generate more sequence data, close gaps, correct misassemblies or make other improvements to the assembly. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site.Ī genome assembly is the specific set of nucleotide sequences used to represent an organism's genome. 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. The NCBI Assembly database ( provides stable accessioning and data tracking for genome assembly data. ![]()
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