GetData
Get microbiome data from various repos
Installation
To install this package, first install deblur and sra-tools
conda install -c bioconda sra-tools deblur
Then you can install this repository via
pip install git+https://github.com/mortonjt/GetData.git
Retrieving and Deblurring amplicon studies on the Sequence Read Archive
Run process_experiment.py for the full help menu.
process_experiment.py takes as input an SRA table.
See here for an example of one of these tables (it can be downloaded under the Download Metadata) button.
process_experiment.py -i SraRunTable.txt --deblur-path `which deblur` -p `dirname $(which deblur)` --num-threads 40
Obtaining SRA Run Tables
These tables can be obtained through using the SRA search engine.
For example, if one wanted to look up the sequencing data for this paper
they can go to the SRA website, and search under SRA -> Personalized Nutrition by Prediction of Glycemic Responses.
The SRA download page can be found under Send results to Run selector. Most of the time this will only contain a subset of the sample metadata,
so that information will need to be retrieved from either supplemental materials from the paper or from the authors directly.
Notes
This has been tested on fastq-dump 2.8.0