Download and extract SRA data
Use the scripts prefetch-sra.bash and fastq-dump-sra.bash to download and extract data from the sequence read archive. They require a list of accession numbers for sequencing runs, usually in the form of an SRR_Acc_List.txt.
Extract info on runs from SraRunTable.txt
Adapt and use the script SraRunTable2config.py to extract relevant info from a SraRunTable.txt and parse it into YAML format as a starting point for a Snakemake config.yaml.
TODOs
- turn as much of this as possible into a Snakemake pipeline, to improve reproducibility, parallelisation and documentation