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[Feature request] Use NCBI datasets to download input files #62

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elhossary opened this issue Apr 7, 2024 · 0 comments
Open

[Feature request] Use NCBI datasets to download input files #62

elhossary opened this issue Apr 7, 2024 · 0 comments

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@elhossary
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NCBI has an extremely useful tool to download reference genomes, annotations, and reads from their repositories with much less hassle.
https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/datasets/

The idea is to integrate this tool in make READemption automatically download the input files.
image

example command that can be wrapped inside READemption:

./datasets download genome taxon human --reference --chromosomes 1 --filename human_chr1.zip --include genome,gff3
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@elhossary