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. 2014 Jan;42(Database issue):D38-43.
doi: 10.1093/nar/gkt1082. Epub 2013 Nov 8.

Assembly information services in the European Nucleotide Archive

Nima Pakseresht  1 , Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li, Xin Liu, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Stephane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dmitriy Smirnov, Silvano Squizzato, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
Affiliations

Assembly information services in the European Nucleotide Archive

Nima Pakseresht et al. Nucleic Acids Res. 2014 Jan.

Abstract

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the world public domain nucleotide sequence data output. ENA content covers a spectrum of data types including raw reads, assembly data and functional annotation. ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets. This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many enhancements have already been made available over the year to components of the submission service. In this article, we briefly review ENA content and growth over 2013, describe our rapidly developing services for genome assembly information and outline further major developments over the last year.

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Figures

Figure 1.
Figure 1.
The figure presents the number of genome assembly submissions over time.
Figure 2.
Figure 2.
The figure provides a screen shot of an assembly record made visible following a typical search in which the user clicked the ‘Advanced Search’ link from the homepage, checked the ‘assembly’ domain radio button, searched for human genome using organism name ‘human’ and selected GCA_000001405.14 from the listed results. This page provides an assembly description, assembly statistics for all the assembly versions, links to all chromosomes, alternative loci, patches and pseudoautosomal regions in the assembly and references.
Figure 3.
Figure 3.
A result table containing selected fields for Caenorhabditis elegans results from the sequence domain.
See this image and copyright information in PMC

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