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pachterlab / seqspec

machine-readable file format for genomic library sequence and structure
MIT License
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Sequencing data repositories which accept seqspec? #8

Closed photocyte closed 1 year ago

photocyte commented 1 year ago

Hi there,

Is there any list of sequencing data repositories which accept seqspec? (realizing that seqspec is very new, and direct support is unlikely at this stage, but maybe there are some best practices even at this point?)

For example, does NCBI SRA accept seqspec?

detrout commented 1 year ago

The IGVF DACC is currently planning on using it as they build a portal for this project.

IGVF is what motivated https://github.com/IGVF/seqspec/pull/2

sbooeshaghi commented 1 year ago

Hi @photocyte, this is definitely a goal we are aiming for with seqspec. For now, we advise users to generate seqspec specification files for their data and make them available (one way is through a PR to this repo (under assays)!).