NCBI Mass Sequence Downloader


This program will download sequences en masse from several NCBI databases (at the user's chioce). After the downloading is finished, the program will check the resulting file for any missing sequences and continuously retry the download until all sequences are present in the local file. It will run on both python2 and python3.

NCBI Data Usage Policies and Disclaimers may apply to downloaded data.


If you use NCBI Mass Sequence Downloader in your research, please cite the following paper: Pina-Martins, F., & Paulo, O. S. (2016). NCBI Mass Sequence Downloader–Large dataset downloading made easy. SoftwareX, 5, 80–83.


  • Pyhton (2 or 3) (and the standard lib);
  • PyQt5 for the GUI version.
  • Requests

Where to get it


Bug reporting

Found a br or would like a feature added? Or maybe drop some feedback? Just open a new issue.