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[Feature request] Use NCBI datasets to download input files

Open elhossary opened this issue 1 year ago • 0 comments

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

elhossary avatar Apr 07 '24 15:04 elhossary