Assembly: a resource for assembled genomes at NCBI

By P. Kitts, D. Church, Françoise Thibaud-Nissen, Jinna Choi, Vichet Hem, V. Sapojnikov, Robert G. Smith, Tatiana A. Tatusova, Charlie Xiang, Andrey Zherikov and 4 more. Nucleic Acids Res., 2015

359 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy (2021, methodology): “However, starting with GTDB R05-RS95, the GTDB only incorporates genomes from the NCBI Assembly database (8) and explicitly excludes assemblies annotated as being from ‘large multi-isolate projects’ at NCBI as these comprise genomically well-represented species and would require substantial addition”
Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets (2024, neutral): “Genome data packages are available for the nearly two million eukaryotic and prokar-yotic assembled genomes and encompass genomic, transcript, and protein sequences, as well as genome annotation files for all GenBank and NCBI RefSeq genomes stored in the NCBI Assembly database 6 .”
KEGG for taxonomy-based analysis of pathways and genomes (2022, neutral): “It is available for the genomes with the NCBI assembly level of ‘Complete genome’ and ‘Chromosome’ (10) covering about half of eukaryotic genomes and almost all prokaryotic genomes in KEGG.”
Database resources of the National Center for Biotechnology Information. (2019, background): “gov/assembly/) (10) by default; however, an option is provided to clear the filter and view all assemblies matching the query.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016, background): “Genomes are obtained from public data repositories, including NCBI (13) and UCSC (14).”
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, background): “The reference and representative set can be searched in Entrez Assembly (23) (https://www.”
Database resources of the National Center for Biotechnology Information (2014, background): “The common data unit within these three directories is a subdirectory corresponding to a record in the Assembly database (3) and given a name consisting of the Assembly accession followed by the name of the assembly.”
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly (2016, neutral): “In a second analysis, we used the same collection of ClinVar variants ( n = 113,368) to evaluate the impact of assembly updates on the remapping of data from GRCh37 to GRCh38.”