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scf trace assembly
DNA contig assembly

454 Easy SFF Tools

The way the bioinformatics programs should be...




Program description


SFF Workbench (initial name '454 SFF Tools') 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 commands in an obscure text console.





SFF Viewer:

  • Blazing fast
  • Compact/portable (no installation required)
  • Works under guest/limited accounts (you don't need admin password)
  • User-friendly graphic interface
  • Easy to use file browser (allows you to quickly locate and view SFF files)
  • 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 mini-chromatograms
  • Display low quality (clipped) ends in dark gray color

SFF Editor:

  • Delete samples
  • Convert SFF to multiFASTA format
  • Cut a SFF file in smaller pieces
  • Sort samples by name, average quality and length
  • Append Roche index to unindexed files


The program loads a 400MB SFF file (containing over 122000 samples) in only 4.51 seconds. It requires only 34MB of memory to load the graphic interface and to display the entire content of the file. Because the file is cached, consecutive attempts to load the same file will require only 1.9 seconds.

The test was performed on a Qosmio x505 laptop (Intel i5 CPU @ 2.2 GHz, 3GB or RAM, low end hard drive) running Win 7 32 bits.


More features...
  • It doesn't alter original files
  • Buffered files for faster disk access
  • The index can be saved to external file (when internal index format is unknown)
  • Automatically append Roche index back to all generated files
  • Save as MultiFasta
  • Save as SFF
  • Sort by 'Average quality'
  • Sort by 'Length after trim'
  • Sort by 'Name'
  • Split SFF files in smaller blocks
  • Allows the user to 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 new
Package size ~ 6 MB
Download time less than 10 seconds (for DSL)
SFF converter - Free download



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 samples 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...

This tool is Free sequence analysis software. Please help us make it better. Let us know if you have any feature requests and we will try to integrate them.


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Chromatogram Explorer
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DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation. You can view the chromatograms while browsing through folders using its integrated file explorer. With a single click you can trim the low quality bases at the end of your samples.

Everything to FASTA converter
multi-FASTA to FASTA

Everything to Fasta Converter converts the specified samples (SCF, ABI, FASTA, multiFasta, GBK, multiGBK, SEQ, TXT) to FASTA format. Starting with version 3.0 protein FASTA files are also supported.



SFF details:

Standard flowgram format (SFF) is the file format used to store results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing.

sequence assembling software
contig assembly software