Assembly


26578580	Assembly: a resource for assembled genomes at NCBI. [PMID: 26578580] Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V, Sapojnikov V, Smith RG, Tatusova T, Xiang C, Zherikov A, DiCuccio M, Murphy TD, Pruitt KD, Kimchi A. 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. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US. Nucleic Acids Res. 2016:44(D1) \| 209 Citations (from Europe PMC, 2025-03-29)

Assembly: a resource for assembled genomes at NCBI. [PMID: 26578580]

Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V, Sapojnikov V, Smith RG, Tatusova T, Xiang C, Zherikov A, DiCuccio M, Murphy TD, Pruitt KD, Kimchi A.

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. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Nucleic Acids Res. 2016:44(D1) | 209 Citations (from Europe PMC, 2025-03-29)

URL:	http://www.ncbi.nlm.nih.gov/assembly/
Full name:
Description:	The NCBI Assembly database provides stable accessioning and data tracking for genome assembly data.
Year founded:	2016
Last update:	2015-08-30
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Animal Archaea Bacteria Fungi Plant Virus
Database category:	Gene genome and annotation Metadata Raw bio-data
Major species:	Homo sapiens Bos taurus
Keywords:	genome

University/Institution:	National Center for Biotechnology Information
Address:	Bethesda, MD 20894, USA
City:	Bethesda
Province/State:	MD
Country/Region:	United States
Contact name (PI/Team):	Paul A. Kitts
Contact email (PI/Helpdesk):	kitts@ncbi.nlm.nih.gov

Database Commons
a catalog of worldwide biological databases

a catalog of worldwide biological databases

Database Profile

General information

Classification & Tag

Contact information

Publications

Ranking

Community reviews

Word cloud

Tags

Related Databases

Record metadata

Research & Resources

Featured

Alliance & Collaboration

Conference & Outreach

About

Database Commons a catalog of worldwide biological databases