New tools to download data from ENA

New tools to download data from ENA

23 Jun 2017 - 14:17

We have been listening to feedback from the ENA user community and are pleased to announce that we now offer two tools to make retrieving data from ENA much easier.

ENA Browser Tools

enaBrowserTools is actually a suite of tools providing support for downloading sequence data for a given accession. There are two main tools within this suite: enaDataGet and enaGroupGet.

enaDataGet

This tool will download all data for a given sequence, assembly, WGS set, run, experiment or analysis accession. When downloading an assemby, read, experiment or analysis, a new directory will be created to hold all the files. You can choose which format you want to download for each type of data record, for example FASTA format for a WGS set or submitted files for a run.

Examples of use

1. Download the latest version of the Mycobacterium bovis, MB4, WGS project CDHE01000000 data:

enaDataGet -f fasta CDHE01

Note that you could also use CDHE, CDHE01000000, and CDHE00000000 to download this set.

2. Download the A/England/8/2009 strain Influenza A genome assembly (GCA_000986055) in embl (Flat file) format:

enaDataGet GCA_000986055

 

enaGroupGet

This tool will allow you to download all data of a particular group (sequence, WGS, assembly, read or analysis) for a given sample or study accession. A new directory will be created using the supplied sample/study accession as the directory name.

Example of use

Download the read data in FASTQ format for the Local surveillance of infectious diseases and antimicrobial resistance from sewage project:

enaGroupGet -g read -f fastq PRJEB13832

 

ENA FTP Downloader

The ENA FTP Downloader is a Java application that can be downloaded onto your computer and provides a graphical user interface to obtain read and analysis files from ENA. This application will be familiar for users of the bulk download tool within the ENA Browser. You can download files via two methods:

  1. Provide the accession of interest; or
  2. Upload a report file that you have retrieved from ENA's portal API or advanced search.

We are particularly excited about the second option as it now allows you to define a set of data that is of interest to you, such as finding all reads available for a given tax ID, and share this report with collaborators, knowing that everyone will be able to easily download exactly the same set of files.

Downloading the new tools

Both of these new tools are available in public GitHub repositories.  You can download the latest code available at the time, but we recommend visiting the Releases section for the lastest release.

ENA Browser Tools: https://github.com/enasequence/enaBrowserTools

ENA FTP Downloader: https://github.com/enasequence/ena-ftp-downloader

Coming Soon

We have plans to add to each of these tools in the coming weeks and months, so stay tuned. Plans include:

  • Add support for tax IDs in enaGroupGet
  • Allow a search report to be generated from within the ENA FTP Downloader

Subscribe to the e-mail newsletter
Get a monthly round-up of the hottest news and features from EMBL, straight to your inbox.
Or stay updated with the RSS feed (EMBL-EBI only).