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scf trace assembly
DNA contig assembly

454 SFF viewer/converto tool

The way the bioinformatics should be...




Program description


454 SFF Workbench is an easy to use SFF file viewer, editor and converter. SFF Workbench is the first and only SFF editor with graphic interface on the entire bioinformatics market! With this tool we wanted to help the biologists to concentrate on their work instead of wasting time poking obscure commands in a console.





SFF Viewer:

  • Display SFF file details (size, total number of samples/reads, key sequence, flow characters)
  • Display Roche details (index, manifest)
  • Display the average quality of each sample (before and after end trimming)
  • Display the sample length (before and after end trimming)
  • Display quality values
  • Display low quality/clipped ends in gray color
  • User-friendly graphic interface. Compact/portable (no installation required, no admin password required
  • Easy to use file browser (allows you to quickly locate and view SFF files)

SFF Editor:

  • Split huge FastQ/SFF file in chunks of x reads
  • Convert SFF to FastQ
  • Convert SFF to Fasta
  • Convert FastQ to Fasta (multiFasta)
  • Trim poly-A/T tails
  • Cut reads with average QV under specified threshold
  • Cut reads if they contain N bases (the user can specify how many)
  • Cut reads that are too short
  • Cut reads that are too long
  • Cut low complexity reads
  • Trim low quality ends. Automatically detect and cut low quality bases at the end of each read.
  • Split multiplexed files (MID/Barcode splitter)
  • Dereplicate sequences


454 SFF Workbench loads a 400MB SFF file (containing over 122000 samples) in only 2.5 seconds. It requires only 34MB of memory to display the entire content of the file. The test was performed on a Intel i5 @2.2 GHz, 3GB or RAM, low end hard drive running Windows 7.


More features...
  • It doesn't alter the original SFF file
  • Buffered files for faster disk access
  • The SFF index can be saved to external file (when internal index format is unknown)
  • Automatically append Roche index back to all generated SFF files
  • Convert SFF to FastQ/multiFASTA
  • Save as SFF
  • Sort by 'Average read quality'
  • Sort by 'Length after clip'
  • Sort by 'Read name'
  • Split SFF files in smaller blocks
  • The user can select and delete multiple reads
  • Remember last state (GUI position, user settings, last open folder, etc)
  • Works with very large files (over 6GB)

More screenshots...

Do you want to see more screenshots? Then click here.

SFF file viewer, SFF editor, SFF to FASTA converter




Name SFF Workbench
Version 1.5.1
Date 11.2013
Package size ~ 6 MB
Download time less than 10 seconds (for DSL)

SFF converter - Free download

NOTE! This tool has been replaced by
NextGen SFF/FastQ Workbench



What's new in this version...

News: The speed and memory requirements have been dramatically improved since v1.0! Opening 2GB files requires less than 80MB or RAM.

What's in the package/How to install it...

SFF Workbench is delivered in a small package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

SFF Workbench installs in any computer even if you don't have administrator rights. To uninstall SFF Workbench, just delete it.

How to use it...

A small introduction on how to use the program is available here.

Please note that the demo version of the program will not process all reads in a SFF file. Upon program registration this limitation will be removed.


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.

Instant feedback...

Please help us make SFF Workbench better. Let us know if you have any feature requests and we will try to integrate them.


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