View SCF files in your browser
The open trace format of the Staden package, which many sequencing tools read and write. Open one right here as its trace. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your read opens as its four curves, with the bases called and a quality bar for each.
- A, C, G and T in their colors • Calls and quality bars
- Zoom along the read • Taller or lower peaks
- Find bases on either strand • The reverse complement a click away
- Export • Save the read as FASTA or FASTQ
About SCF
Simon Dear and Rodger Staden published the Standard Chromatogram Format in 1992 so traces from any sequencer could be read by any tool. The Staden package, Phred and other basecallers read and write it, and older archives and some pipelines keep their reads in it.
An SCF holds the four curves, the bases with where each peak is and how likely each one is to be right, and comments such as the sample's name and the machine. Version 3 stores the curves as differences, which pack smaller.
Filepeek reads versions 2 and 3 in your browser and draws them like an AB1: the curves in A green, C blue, G black and T red, the calls with a quality bar each, zoom for the read and the peaks, Find for bases on either strand, and the reverse complement. Export saves the read as FASTA or FASTQ.
Standard Chromatogram Format trace
.scf
Format
- MIME type
- application/x-scf
- Made by
- Simon Dear and Rodger Staden, at the MRC Laboratory of Molecular Biology
- Released
- 1992
Inside the file
- Curves
- A, C, G and T
- Calls
- Bases, peaks and how sure each is
- Comments
- The sample's name and the machine
- Versions
- 2 and 3
Opens in every browser
Filepeek opens SCF files in Chrome, Edge, Firefox and Safari. On their own, browsers only download them.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open SCF
- WindowsChromas • The Staden package's Trev
- MacThe Staden package
- iPhone and iPadNo app opens it
- AndroidNo app opens it
Questions
Is an SCF file the same as an AB1?
It holds the same read, its curves, calls and qualities, in an open layout instead of Applied Biosystems' own. Staden's convert_trace turns one into the other, and both open here the same way.
Can I save the bases with their qualities?
Yes. Choose Export, then Save as FASTQ, which keeps a quality for each base, or Save as FASTA for the bases alone.