NCBI Closes Sequence Read Archive, Pepidome Respository

By Bio-IT World Staff

March 1, 2011 | NCBI has announced that it will discontinue its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data and the Pepidome Repository, citing budgetary constraints. 

Closer of SRA and the Trace Archive will occur in phases, with all submissions ceasing within the next 12 months. The Pepidome Repository online browser, query and display interfaces are scheduled to be closed within weeks, with existing data and metadata files available on the NCBI ftp server. NCBI announced the discontinuations in a statement on its website in mid-February.

Over the next several months, NCBI will be working with staff from NIH Institutes that fund large-scale sequencing efforts to develop an approach for future access to and storage of the existing data, the statement said.

"NCBI will continue to support and develop information resources for biological data derived from next-generation sequencing such as genotypes, common variations, rare variations, sequence assemblies and gene expression data. We therefore encourage the research community to continue submissions of these data to the applicable databases," read the statement, listing RNA-Seq and epigenomic data to GEO; Variants, genotypes, phased haplotypes, and polymorphisms to dbVar, dbGaP and dbSNP; Genomic assemblies to GenBank/WGS; Transcript assemblies to GenBank/TSA; and 16S ribosomal RNA and other targeted locus survey assemblies to GenBank.