Python module to search, fetch and filter records from NCBI's Sequence Read Archive. In addition to the search options available on SRA it makes it possible to filter by read length or library layout. Outputs a CSV file.
Requirements:
Quick and rough:
./sra.py -s "agalma[Organism]" -m 3 -o sra_output -e [email protected]
For a more refined filtering check out fetch_sra.py.
Parsed fields of an SRA record that are exposed to filtering: accession, title, study title, library strategy, library layout, instrument model, taxon id, scientific name, taxonomic lineage, run accession, total spots, total bases, size, published, nreads, read average.