What is a chromatogram

A chromatogram (sometimes also called electropherogram) is the visual representation of a DNA sample produced by a sequencing machine (like Applied Biosystems ABI PRISM 7700 Sequence Detection System).

Fig. 1 - Example of chromatogram. The green bars indicate this chromatogram has a very high quality.

Chromatogram files can be easily converted to ABI, FASTA or SEQ with tools like DNA Baser Sequence Assembler, DNA Chromatogram Explorer, Batch ABI to FASTA converter. Please see the Download page for details.

DNA Baser Sequence Assembler

DNA Baser Sequence Assembler supports SCF and ABI (ABI, AB, AB!, AB1) chromatogram files. To open a chromatogram file just double click on it in Project Manager or drag it from Windows Explorer in DNA Baser Sequence Assembler.

Details about chromatogram files

• What is a good chromatogram
• FAQ about quality values (QV)
• Automatic low quality ends trimming
• Untrusted regions

FAQ about chromatograms

Some of my ABI chromatogram files are corrupted

ABI format was invented long time ago. It can be considered an obsolete format because it has problems in storing large sequences/chromatograms. Often the ABI files generated by some machines are corrupted. When DNA Baser Sequence Assembler encounters a corrupted chromatogram, it will automatically try to restore the data and it will write a report (in the same folder where the file is located) for that corrupted chromatogram file.

Why the SCF format is better than ABI format?

Not only that SCF format do not have the above-mentioned bug, but it offers many other additional features. In addition, the SCF format was designed to be easily compressed (using programs like WinRar or WinZip). This is very important for companies storing large amounts of chromatogram files.
We strongly recommend you to use the SCF format instead of ABI.

More DNA sample file converters

• Multi-FASTA to FASTA converter
• FASTA to Multi-FASTA converter

About HeracleSoftware

HeracleSoftware provides effective, biologist friendly, easy-to-use sequence assembly and analysis software tools to meet the ever changing needs of today’s genetic/medical researcher and diagnostician. All of our software tools are the result of close, effective collaborations with the genetic community. Therefore, if one of our software programs doesn't meet your exact needs, please do not hesitate to contact us.