Selects 100 oyster (Magallana / Crassostrea) sequencing experiments from an NCBI SRA search export and downloads them.
| Task | Code | Output |
|---|---|---|
01 Select 100 experiments from data/sra_result.csv |
code/01-select-experiments.py |
output/01/ |
| 02 Download the selected experiments from NCBI SRA | code/02-download-sra-data.py |
output/02/ (data not tracked in git) |
Task descriptions are in Tasks.txt; repository conventions are in Instructions.txt.
pip install -r requirements.txt # pandas
conda install -c bioconda sra-tools pigz # needed for Task 02 only
Scripts can be run from any directory.
python3 code/01-select-experiments.py
python3 code/02-download-sra-data.py --threads 8
Task 02 downloads about 525 GB of SRA data and needs substantially more free space while converting to FASTQ. It can be re-run to resume.