FAQ about quality values
(QV)
What is the quality value (QV)?
The quality values (also called bases trust information/confidence values) is a number assigned to each base in chromatogram that shows how much
that base is trusted. A small QV means that the predicted base can’t be trusted too much (the base caller may be wrong). The QV can
have any value from 0 to 100. A high QV
means that the base can be trusted. By default DNA Baser considers a base untrusted if its QV is under 25-30.
How important is the QV for DNA Baser Sequence Assembler?
DNA Baser Sequence Assembler is the only software on the market that automates the sequence assembly process reducing the required time
with about 1000%.
In order to generate high quality/trustable contigs WITHOUT any human intervention, DNA Baser Sequence Assembly relies on the quality value (QV) information assigned to each
base as follows:
1)
Usually bases of low quality are gathered at the ends of your samples. These clusters of low quality bases are called untrusted regions. When performing
sequence assembly or other DNA sequence analysis, the user have to manually cut
out (trim) those bases from samples, else the assembly may be very poor (too many ambiguities) or even wrong. This is a time consuming process!
DNA Baser Sequence Assembler can automatically trim the untrusted regions before it assembles
the sequences.
2) During sequence assembly, if an ambiguity is encountered, DNA Baser Sequence Assembler will use the QV information
to automatically correct the ambiguity for you.
If the QV information is missing, DNA Baser will not
automatically trim the untrusted regions. In this case the user will have to inpect the contig an check if the suggestions made by DNA Baser are correct.
Which are the formats that can store quality value information?
Only SCF and ABI sample file types can store QV information. FASTA, SEQ and TXT files cannot store this information.
If I have ABI or SCF files, it means implicitly they contain QV?
Not necessarily. If your sequencing machine is set to generate SCF files, those files will certainly (99.9%) contain QV information. If your sequencing machine is set to generate
ABI chromatogram files, then in some cases the generated chromatogram files may not contain quality value (QV) information. However, your technician can fix this easily by setting the
machine to store quality values in your ABI chromatogram files.
What to do in case your ABI files do not have QV filed included?
Always use the SCF files instead of ABI files as SCF format always has the QV included. If you do not have the SCF files, please instruct your technicians to set the machine to generate
not only ABI files but also SCF files. This is a very simple procedure. All you have to do is to check a checkbox in the machine’s (software) interface. In addition, your technician
can instruct the software to generate ABI file WITH QV included.
Why DNA Baser assembler does not automatically trim the low quality regions in my chromatograms?
Usually you don't have to manually trim the ambiguous bases (the 'N's) from your sequences. DNA Baser will clean the end automatically for you BUT ONLY IF the quality values are included
in the file. SCF files always contain QV. ABI files only sometimes have this information included. You can instruct your sequencing machine to always generate ABI files with QV included
(you just need to check a checkbox in your machine's interface).
How can I find out if my samples contain information about quality values (QV)?
With DNA Baser, it is very easy to get this information: double click an ABI/SCF file to open it in DNA Baser. If you see green columns above each base in chromatogram, then your file
has the quality value field included.
Fig 1. ABI file with QV included
Fig 2. ABI file without QV included (green bars indicating the quality of each base are missing)
Another way to check the existence of quality value is to see the properties of a file. Press Control+Enter to see the properties dialog:
 
If my samples do not contain quality values, does it mean that I can’t make a contig?
In most cases, DNA Baser will be able to generate contigs without problems even if your samples does not contain QV field. However in some very rare cases (especially when your samples
are extremely poor), DNA Baser may not succeed to create contig. In this case, you must manually trim the untrusted ends of your samples/chromatograms.
Can I mix ABI and SCF files?
Sure. You can assemble ABI, SCF, FASTA, SEQ files together.
Can I mix samples containing QV with samples that do not contain QV (like SCF and FASTA)?
Yes. However, DNA Baser will create the contig in non-QV mode. It may be better to totally remove that file from contig than to use it. See the table below:
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How many files contain QV info?
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Contig will be done in:
|
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All
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QV mode
|
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None
|
non-QV mode
|
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Some
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non-QV mode
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In rare situations, DNA Baser generates poor contigs. Why?
Because your files contain no QV information. You may need to trim the untrusted regions manually.
Related topics
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