geofetch is a command-line tool that does two things when given one or more GEO/SRA accessions:
Downloads either raw or processed data from either GEO or SRA
Produces a standardized PEP sample annotation sheet of public metadata. This makes it really easy to run looper-compatible pipelines on public datasets by handling data acquisition and metadata formatting and standardization for you.
You can use it with the sra_convert pipeline, a pypiper pipeline that converts SRA files into BAM files.
pip install geofetch
Now, run it on the command line:
Next, check out the usage reference, or for a detailed walkthrough, head on over to the tutorial.
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