Sra Replacement

Question

[Science_Robot]

Now that the SRA is getting shut down, how do you plan on sharing your reads?

[Casey Bergman]

This question is no longer relevant since "NCBI will continue to operate the SRA as NIH's primary archive of high-throughput sequencing data": http://www.ncbi.nlm.nih.gov/About/news/13Oct2011.html

[Science_Robot]

Did you read that link before posting it?

They are only continuing to host 3 types of data. It is no longer a repository for short reads. They are only hosting: assemblies, epigenomic data, and 16S rRNA amplicons.

Answer 1

[David L.]

The [?]European Nucleotide Archive[?] might be an option.

EMBL-EBI will continue to operate its SRA according to http://www.ebi.ac.uk/ena/SRA_announcement_Feb_2011.pdf .

Answer 2

[Nakao]

and also DDBJ will continue Sequence Raw Data Archiving

Answer 3

[Joachim]

From http://www.ncbi.nlm.nih.gov/sra:

We therefore encourage the research community to continue submissions of these data to the applicable databases, including:

1. RNA-Seq and epigenomic data to GEO
2. Variants, genotypes, phased haplotypes, and polymorphisms to dbVar, dbGaP and dbSNP
3. Genomic assemblies to GenBank/WGS
4. Transcript assemblies to GenBank/TSA
5. 16S ribosomal RNA and other targeted
6. locus survey assemblies to GenBank

[Science_Robot]

None of those things are for reads data except for maybe 16S.

[Ian]

I agree with 'audyyy' SRA now does not have any facility for DNA reads, e.g. ChIP-seq.

Answer 4

[Casey Bergman]

In time, I believe BioTorrents may seen to be a viable option for hosting raw sequencing data.