Hi @zeylanicus
These reads are in SRA, correct?
That means you can use a tool like this → Faster Download and Extract Reads in FASTQ format from NCBI SRA. Getting Data into Galaxy
These tutorials show some super automated ways to handled batch data. These go from publication identifiers, to read retrieval, through full analysis and graphics. Maybe portions of these you can reuse or customize or just get ideas from. GTN Materials Search (query=sra)
Hope this helps! 