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Downloading-sequence-data-from-ENA

enaFastqFetch.py can be used to query the ENA for different types of data and bulk download the associated fastq files.

CAUTION: Please be aware you may be downloading very large datasets. Before downloading the fastqs, the program will print to the terminal the total size of the files to be downloaded.

Usage

usage: enaFastqFetch.py [-h] -s SEARCH -d DATATYPE [-n NUMRUNS]

optional arguments:
-h, --help            show this help message and exit
-s SEARCH, --search-term SEARCH
                      term you wish to search for, e.g. Mycobacterium, 1763,
                      SRR5188398, SRX2504319, PRJNA360902, SELEX
-d DATATYPE, --data-type DATATYPE
                      datatype you wish to search for, e.g. run, study,
                      experiment, sample
-n NUMDOWN, --num-downloads NUMDOWN
                      number of runs/studies/experiments/samples you wish to
                      download
-r, --report-file     generate a report file

How enaFastqFetch.py works

enaFastqFetch works by querying the ENA's API for the corresponding XML file, then text mining the XML for the fastq download links. By providing enaFastqFetch with a search term and datatype it will automatically download the fastqs associated with your request.

Search term

The search term is specified through the -s flag. You can search for data by using its accession ID, taxon ID, or by using free text searches.

Datatype

The datatype is specified through the -d flag. The following values are valid: run, study, experiment, sample. The ENA uses a hierarchical system to define the datatype:

  • STUDY: A study defines an overarching investigation. In most cases it's a dataset associated with a publication.
  • SAMPLE: A sample is a biological sample which is used in a study.
  • EXPERIMENT: An experiment is conducted on a sample. This defines things like the instrument used for sequencing and the library preparation.
  • RUN: A run is the actual sequencing reads which are associated with a sample and experiment. I.e. these are the fastq files.

So for example the run SRR3206414 is associated with the sample SRS1318643 and the experiment SRX1615315, and overall it belongs to the study SRP071047/PRJNA313382.

Number of runs/studies/experiments/samples to download

The number of runs/studies/experiments/samples to download can be specified using the -n flag. This flag is optional. If not specified, all the data which matches the requested search term will be downloaded.

Report file

A report file including information on the downloaded data will be generated if you pass the --report-file flag.

Examples of using the accession ID to download

E.g. to download the fastq associated with the run SRR5188398:

enaFastqFetch.py -s SRR5188398 -d run

E.g. to download all of the fastqs associated with the study PRJNA360902:

enaFastqFetch.py -s PRJNA360902 -d study

E.g. to download all of the fastqs associated with the experiment SRX2504319:

enaFastqFetch.py -s SRX2504319 -d experiment

E.g. to download all of the fastqs associated with the sample SAMN06240265:

enaFastqFetch.py -s SAMN06240265 -d sample

Examples of using the taxon ID to download

E.g. to download all the runs found for the taxon 47839:

enaFastqFetch.py -s 47839 -d run

E.g. to download 10 runs for the taxon 1773 and generate a report file:

enaFastqFetch.py -s 1773 -d run -n 10 --report-file

Examples of using free text search to download

E.g. to download 5 selex studies:

enaFastqFetch.py -s "SELEX" -d study -n 5