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How to online sketch an SRA accession without downloading? #3337

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mr-eyes opened this issue Sep 25, 2024 · 1 comment
Open

How to online sketch an SRA accession without downloading? #3337

mr-eyes opened this issue Sep 25, 2024 · 1 comment
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@mr-eyes
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mr-eyes commented Sep 25, 2024

This command will stream the fasta file (whether SE or PE) to sourmash for sketching.

fasterq-dump --fasta-unsorted ${sra_accession} --stdout | sourmash sketch dna - ....
@mr-eyes mr-eyes added doc documentation content or issues fyi Information that is interesting or useful labels Sep 25, 2024
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ctb commented Sep 25, 2024

relevant: #2941

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