Hopper: software for automating data tracking and flow in DNA sequencing.
BACKGROUND
Genome-scale DNA sequencing is a multistep process in which large numbers of small template clones are propagated, purified, sequenced and analyzed on acrylamide gels. A significant challenge to these projects is the scale at which the data handling must be done. Hence, large-scale sequencing facilities will benefit from tracking template DNA information (purification methods, reaction and electrophoresis conditions) in a systematic fashion. A lack of software tools that support automated sample entry, and automatic data storage, retrieval and analysis are a major hindrance to recording and using laboratory workflow information to monitor the overall quality of data production.


RESULTS
The UNIX file system has been used to prototype automation of the flow of data from the ABI sequencer to a data repository. Data are automatically processed by a central Perl program, Hopper, which runs a series of programs that analyze data quality (read length estimate, fraction of indeterminate bases, and number of contaminating and repetitive sequences), assemble shotgun sequence data, and generates simple reports describing the results.
Smith
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Department of Molecular Biotechnology, University of Washington, Seattle 98195, USA. T.M.Smith, soundbat@u.washington.edu
Abajian
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Hood
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D003628:Database Management Systems; D005069:Evaluation Studies as Topic; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software; D012985:Software Design