NextGen SFF demultiplexing tool
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FastQ convertor
Convert SFF file

NCBI BLAST DB Downloader

The way bioinformatics should be...






Target database are a key component of a standalone BLAST setup. A common set of pre-formatted NCBI BLAST databases is available from NCBI. NCBI BLAST DB Downloader is a a freeware tool that automates the NCBI BLAST DB download process. It automatically downloads and unpacks the selected NCBI Blast databases from NCBI ftp server.


Note: Databases can also be prepared de novo from custom FASTA sequences locally using our Database Builder utility.




  • User can choose which DB to download
  • User can choose where to download the databases
  • User can enter the path where Blast is installed
  • Usee can choose the Temp folder
  • Show download progress, estimated time to finish the download, download speed (kb/sec)
  • Check if enough disks pace before download
  • Allow resuming the download
  • Remember GUI settings upon restart
  • Announce user when a new DB is available (on NCBI ftp)
  • Automatically start download upon program start up

Visual FastQ file viewer & converter


FastQ dereplicate



NCBI BLAST DB Downloader

Download time

< 10 seconds


27 March 2015

Sequence Workbench is now part of the Avalanche NextGen package. Please download this package.



  • < 3MB of disk space
  • < 30MB free RAM
  • No Java, no .Net
  • Windows XP and up




This software tool is really small so you can easily copy it on a floppy disk or USB flash stick and take it with you or send it to your colleagues via email.



Similar tools

  • NextGen SFF/FastQ Workbench is an efficient and easy to use FastQ/SFF file viewer, editor, converter, cleaner and demultiplexer. With this tool we wanted to help the biologists to concentrate on their work instead of wasting time poking obscure commands in a console. The program can open huge FastQ/SFF files even when running o a modest computer.
  • NCBI Blaster (aka BLAST Robot) is a software tool that automates the NCBI BLAST search processes.




This tool is Nextgen SFF/fastq analysis software. Please let us know how to make it better.

We are interested in:

  • Feature requests
  • Platform you are interested in (Windows, Mac, Linux)
  • A name for the program :)


SFF to FastQ to FASTA converter