May 26, 2018

Base calling and quality value assignment on DNA sequencing

Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.

Trace data is read from chromatogram files in the SCF, ABI, and EST formats, even if they were compressed using gzip, bzip2, or UNIX compress. Quality values are written to FASTA format files or PHD files, which can be used by the Phrap sequence assembly program in order to increase the accuracy of the assembled sequence.

Base calling and quality value accuracies tested for ABI models 373, 377, and 3700 Molecular Dynamics MegaBACE LI-COR 4000

Base calling accuracies tested for ABI model 3100 Beckman CEQ

It contains also a data evaluation program called ‘daev’. See DAEV.DOC for more information.

You must obtain the tarball via e-mail to build. See the web site below.

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