What are chromatograms

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

Fig. 1 - Example of chromatogram. The green bars above chromatogram peaks high confidence scores.

Importing chromatograms

DNA Sequence Assembler supports SCF and ABI (ABI, AB, AB!, AB1) chromatogram files. To open a chromatogram file just double click it in Project Manager.

Converting chromatograms

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

What is a good chromatogram?

With DNA Baser it is easy to make the difference between a good (trusted) chromatogram and a poor one. Just look at the green bars displayed above each base. These bars represents the confidence scores. A high bar means that the base call can be trusted. A low bar means that the base call cannot be trusted.

Usually, poor chromatograms enter unwanted ambiguities in your contig. However, if you assemble a good chromatogram and a poor one, DNA Baser will know how to extract the useful information from he good chromatogram and give less trust to the bad chromatogram.

Examples

High quality reads

- no ambiguities
- no noise
- peaks very well spaced

Medium quality reads
- some ambiguities
- peaks are still well spaced
- some homopolymeric stretches are not well resolved

Poor quality reads

- some ambiguities

- the difference between noise and signal is very small

- the overall amplitude of the signal is small

- overlapping peaks

- low confidence in bases assignment (low confidence score)

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 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.

Details about chromatogram files

• FAQ about confidence scores (confidence score)
• Automatic low quality ends trimming
• Untrusted regions

About BioSoft

BioSoft 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.