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21 months ago
PeterC_NCBI
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Magic-BLAST is NCBI's BLAST-based next-gen alignment tool. The latest version (1.6.0) has usage reporting, access to SRA in the cloud, taxids in SAM output, file upload of SRA accessions, and other improvements and bug fixes.
Release notes: https://ncbi.github.io/magicblast/release/release.html
Download: https://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/
What was the thought behind adding direct SRA cloud access? Since the data is being downloaded locally that may take some time/space. Hopefully software provides a warning of some sort. What happens if the cloud data is "requester pays" status?
Thanks for the question. Retrieving data from the cloud is fast -- faster and more reliable than from NCBI. The data is streamed from the AWS ODP, which does not have egress charges. There is no need to store data locally. Magic-BlAST streams through them. Magic-BLAST turns of the cacheing feature of the SRA toolkit so that the data aren't saved to your local drive unless you request it with -sra_cache option.
Thanks for clarifying that.
While next question is a bit unrelated I will ask since I have your attention. I recall running into SRA datasets where the only option appeared to be "requestor pays". Are you indicating that ALL SRA data is available to
magic blastvia ODP mechanism?As far as I know all of SRA should be available in AWS ODP and hence free from egress charges as long as you are accessing data there. See our post on this from a while back https://ncbiinsights.ncbi.nlm.nih.gov/2021/02/25/sra-aws-open-data/ I've asked the person in charge of SRA cloud matters to confirm and provide any caveats. Can you provide an example where you see "requestor pays?"
Here is one example where requester needs to pay if they want the original data format submitted by https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR10278808&display=data-access . What data would maagic blast/SRA cloud access download in case of 10x datasets since they are not in standard 1 or 2 file formats?