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. 2016 Jan 4;44(D1):D73-80.
doi: 10.1093/nar/gkv1226. Epub 2015 Nov 17.

Assembly: a resource for assembled genomes at NCBI

Paul A Kitts  1 , Deanna M Church  2 , Françoise Thibaud-Nissen  2 , Jinna Choi  2 , Vichet Hem  2 , Victor Sapojnikov  2 , Robert G Smith  2 , Tatiana Tatusova  2 , Charlie Xiang  2 , Andrey Zherikov  2 , Michael DiCuccio  2 , Terence D Murphy  2 , Kim D Pruitt  2 , Avi Kimchi  2
Affiliations

Assembly: a resource for assembled genomes at NCBI

Paul A Kitts et al. Nucleic Acids Res. .

Abstract

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. 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 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 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 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. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. 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.

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Figures

Figure 1.
Figure 1.
Same name and different sequence content: the Zv7 UCSC and NCBI zebrafish assemblies. Panel A: part of chr21 in the Zv7 zebrafish assembly as displayed in the UCSC genome browser (http://genome.ucsc.edu). Panel B: the same span of chr21 of the Zv7 assembly as displayed in the NCBI Sequence Viewer. The UCSC Zv7 assembly has many Ensembl gene predictions in this region of chr21, whereas the same region in the RefSeq version of Zv7 chr21 at NCBI shows the rb1 and dub genes on the right but no other gene models. The reason for this discrepancy is that NCBI found that one component in this region matched sequences from mouse chromosome X and replaced this foreign component with a gap when they made the RefSeq version of chr21. Zv7 has since been replaced by newer versions of the zebrafish assembly that do not have the mouse contamination.
Figure 2.
Figure 2.
The NCBI genome assembly model. The diagram depicts the assembly organization for a eukaryote with two nuclear chromosomes and a mitochondrial genome. The full assembly is comprised of a primary assembly-unit containing nuclear sequences, a non-nuclear assembly-unit containing mitochondrial sequences and an alternate locus group assembly-unit containing scaffolds that have been aligned to chromosome 2 of the primary assembly.
Figure 3.
Figure 3.
An example of the Assembly details page. The figure shows the upper portion of the cat (Felis catus) genome assembly GCF_000181335.2 page, including the metadata section and global statistics table. This figure does not show the lower portion of the page that contains tables displaying the assembly contents and detailed statistics.
See this image and copyright information in PMC

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