Sraconvert

When you install geofetch, you also get a second utility called sraconvert that handles converting sra data into either bam or fastq format for downstream processing. Sraconvert is essentially a wrapper around NCBI's sra-tools that provides more convenient interface to converting pre-downloaded sra files.

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.

Tutorial

See the tutorial for an example of how to use sraconvert.