freebsd-ports/biology/phred/pkg-descr

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> 2008-05-24 07:04:45 +00:00			`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`