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Automated Trace Quality Assessment
(ATQA) for DNA Sequencing
Description
The explosive growth in the use of DNA sequences in research,
therapeutics, and forensics requires that the quality of the sequence
data be objectively assessable. Daniel H. Wagner Associates has addressed
this need by developing the Automated Trace Quality Assessment (ATQA)
tool.
ATQA provides users with confidence assessments for each basecall
derived from an electrophoretic chromatogram. Confidence scores
are computed by evaluating the quality of the fluorescent trace
data. ATQA assigns four confidence scores to each basecall; the
first three scores separately evaluate the likelihood of substitution,
insertion, and deletion errors. The fourth confidence score corresponds
to the combined probability of an error at the basecall (i.e.,
a substitution or insertion error) or in the gap following the
basecall (a deletion error).
To develop the ATQA tool, Wagner Associates screened hundreds
of numerical features for those most indicative of basecall quality.
We used sophisticated pattern recognition tools and an extensive
training set to partition this feature space and to assign probabilities
of error to each subset.
Uses
- Dramatically reduce time and effort spent in trace editing
- Assess new sequencing technologies and protocols
- Maintain ongoing quality control for existing chemistries
- Improve local and global assembly of DNA fragments
Features
- Three score model (substitution, insertion, and deletion)
provides detailed information about the kind of errors likely
at a location.
Go here for examples of scores with
trace data.
- Trained and tested on an extensive sequence data set from
diverse genetic contexts, sequencing laboratories, and dye chemistries.
Go here for results of ATQA performance
tests.
- Based on the analysis of hundreds of numerical features.
- Easy to understand log scale (0-60) confidence scores.
- Fast execution time.
- Extensive in-house testing and use in the field at the Armed
Forces DNA Identification Laboratory.
Wagner Associates has also applied the same statistical pattern
recognition techniques to the detection of instances of heteroplasmy
or heterozygosity. See our work on mixture
detection. We have an active research project to use ATQA
scores to evaluate the confidence of consensus base calls. See
our work on consensus confidence.
Implementation
ATQA is implemented as a stand alone program with a command
line interface. The program will read user-specified lane files
in SCF and ABI formats. It will compute confidence scores and
write the scores to a user-specified ASCII file or SCF file. ATQA
is currently available for Sun OS, Solaris, Windows 95/98/NT,
Macintosh PowerPC, DEC Alpha, and Linux. Ask us if you are interested
in other ports.
ATQA is integrated with the Staden Assembly Trace Editing software package. Joint users of the Staden package and ATQA can compute and use
ATQA scores from within the Staden package.
We have the experience to provide customized versions of the
library suitable for new electrophoretic-trace-based sequencing
and basecalling technologies. We are also able to provide ATQA
in the form of a callable library suitable for incorporation into
a larger trace editing system.
Purchasing
ATQA
The ATQA system is now available for sale. Go here
for further details.
Contact
Us
We are actively seeking clients and commercialization partners
for the ATQA system.
Please contact atqa@pa.wagner.com
for further information. Go here
for other contact options.
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