SCF File

What are SCF files and how to open them

Are you having problems opening a SCF file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your SCF files.

What is a SCF file?

SCF files have multiple uses, and Altera Synopsys Constraints Format is one of them. Read more about the other uses further down the page.

Altera Synopsys Constraints Format

We have not yet analyzed in detail what these files contain and what they are used for. We're working on it.

How to open SCF files

Important: Different programs may use files with the SCF file extension for different purposes, so unless you are sure which format your SCF file is, you may need to try a few different programs.

While we have not verified the apps ourselves yet, our users have suggested three different SCF openers which you will find listed below.

Last updated: August 13, 2026

All known file formats using extension .SCF

While Altera Synopsys Constraints Format is a popular type of SCF-file, we know of 6 different uses of the .SCF file extension. Different software may use files with the same extension for different types of data.

ChemWindow Standard Chemistry File

We know that one SCF format is ChemWindow Standard Chemistry File. We have not yet analyzed in detail what these files contain and what they are used for. We're working on it.

DNA Sequence Chromatogram

Files in the DNA Sequence Chromatogram format (extension .SCF) are binary trace files produced by DNA sequencing instruments after sample analysis. They record raw fluorescence signal intensities (chromatogram or trace) from a sequencing reaction, plus the identified base sequence, base-position indexes, and quality scores. These files allow researchers to see both the graphical trace data and the base calls, enabling detection of ambiguous calls, sequence errors, or poor-quality regions.

Typical workflow: sequencing machines (or their analysis software) generate .SCF files once base calling and signal processing are completed. Scientists then open these in chromatogram-viewing or sequence-assembly tools to examine sequence accuracy, trim poor-quality ends, compare traces, or export the base sequence (FASTA, SEQ, etc.) for downstream analysis. Some versions (for example SCF version 2.1 and 3.0) support public and private data sections; the public section includes called bases, trace data points, base positions, and quality values, while the private section may include additional instrument-specific metadata such as voltage, current, or raw sensor readings.

Technical identification: .SCF files begin with the ASCII signature ".scf" in the first four bytes (hex 2E 73 63 66) at offset zero.

SCF opener for Windows

We have identified one SCF opener that is compatible with this specific type of SCF file.

Double Commander Shortcuts

We know that one SCF format is Double Commander Shortcuts. We have not yet analyzed in detail what these files contain and what they are used for. We're working on it.

VIA Setup Configuration File

We know that one SCF format is VIA Setup Configuration File. We have not yet analyzed in detail what these files contain and what they are used for. We're working on it.

Windows Explorer Command Shell File

We know that one SCF format is Windows Explorer Command Shell File. We have not yet analyzed in detail what these files contain and what they are used for. We're working on it.

Various apps that use files with this extension

These apps are known to open certain types of SCF files. Remember, different programs may use SCF files for different purposes, so you may need to try out a few of them to be able to open your specific file.

Help us help others

File.org helps thousands of users every day, and we would love to hear from you if you have additional information about SCF file formats, example files, or compatible programs. Please use the links below or email us at submit@file.org to discuss further.