gold2sra.json (152.39 kB)

Gold Stamp IDs to SRA IDs convertion of the metagenomes of GEMs

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posted on 23.11.2020, 13:01 by Moritz Buck
A small simple JSON-file containing the mapping from Gold Stamp IDs from the IMG/JGI database to the SRA IDs useable by fastq-dump to download the corresponding metagenomes from NCBI.
The GoldIDs are the ones from the Supplemental Table 1 from Nayfach, S., Roux, S., Seshadri, R. et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0718-6, that have been submited to the Short Read Archive.
The code used to generate this mapping is available at https://github.com/moritzbuck/jgi2sra_mapper

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