When you install geofetch, you also get a second utility called
sraconvert that handles converting sra data into either
fastq format for downstream processing. Sraconvert is essentially a wrapper around NCBI's sra-tools that provides more convenient interface to converting pre-downloaded
The basic advantages over just using prefetch are:
- it provides the same interface to either download or delete sra files
- it uses the same interface to delete converted files, if desired
- it can automatically delete sra data that has been already converted
- it allows a more flexible specification of locations, using either environment variables or command-line arguments.
This effectively makes it easier to interact with project-level management of sra and fastq data using looper and PEP-compatible projects.
See the how-to SRA to FASTQ for an example of how to use