RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use. Base calling and quality value assignment on DNA sequencing Maintained by:mzaki@biol.s.u-tokyo.ac.jp Port Added: 24 May 2008 07:05:09 License: not specified in port
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.
WWW: http://www.phrap.org/phredphrapconsed.html
New port: biology/consed viewing and editing workbench for sequence
assembly
Consed is a tool for viewing, editing, and finishing sequence
assemblies.
The port is constituted of 4 parts:
biology/phred: base caller with quality evaluation
biology/phrap: sequence assembler for shotgun sequencing
biology/consed: workbench
biology/phd2fasta: small utility
All these can be used separately; however, most function
of consed depends on the others.
Although these programs are licensed freely for academic
and nonprofit purposes, users have to contact the authors
to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at
the time of writing.
PR: ports/118548
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
