getENA

Sometimes we need to download a sequencing project from ENA, fortunately ENA offers in its platform a link to the fastq file that we need. However, we can spend a lot of time downloading files manually if the amount of files is large.

I have developed a small project in python to be able to do this work in an automated and parallel way to increase the performance.

Installation

pip install getENA Alternatively, from GitHub pip install git+https://github.com/EnzoAndree/getENA

Usage

Let's say I'm interested in Clostridium perfringens sequencing projects, we have to search ENA for public sequencing projects at https://www.ebi.ac.uk/ena/browser/text-search?query=clostridium%20perfringens. From there, we choose the codes we need, for example:

PRJNA350702 PRJNA285473 PRJNA508810

We have 2 options to download the FASTQ files, (1) add the project codes to the command line separated by spaces as an argument, or (2) make a file containing a list of all the project codes that need.

For the first option (recommended for few projects for example < 5) we run the following

getENA.py -p PRJNA350702 PRJNA285473 PRJNA508810

For the second option (recommended for many projects e.g. >= 5) we run the following

getENA.py -pfile ena.list.txt

Where ena.list.txt is the file containing a list of all the project codes.

If you want, you can increase the performance by increasing the number of reads that are downloaded in parallel (-t option). However, be careful, because ENA aborts the connection if it detects that you have many connections at the same time with its FTP. Empirically I have observed that 12 parallel connections work properly without ENA cancelling the download.

As a crazy example of many parallel connections of the above commands would be the following:

getENA.py -t 64 -p PRJNA350702 PRJNA285473 PRJNA508810