phred Base calling and quality value assignment on DNA sequencing

0.020425.c biology =0 0.020425.cVersion of this port present on the latest quarterly branch.

RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.

Maintainer: mzaki@m.u-tokyo.ac.jp

Port Added: 2008-05-24 07:05:09

Last Update: 2019-08-13 17:00:39

SVN Revision: 508834

License: not specified in port

Description:

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

SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:

• phred>0:biology/phred

To install the port: cd /usr/ports/biology/phred/ && make install clean

A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted

PKGNAME: phred

Flavors: there is no flavor information for this port.

distinfo:

SHA256 (phred-dist-020425.c-acd.tar.Z) = c7a7773447376c024212b680e1ce1e52c30ad8e18dee317ba863bc10db94f6c9 SIZE (phred-dist-020425.c-acd.tar.Z) = 547645

This port is required by:

for Run

Deleted ports which required this port:

Expand this list of 1 deleted port
1. biology/consed^*
2. Collapse this list of deleted ports.

* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options

===> The following configuration options are available for phred-0.020425.c: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings

Master Sites:

1. There is no master site for this port.

Convert to UCL & cleanup pkg-message (categories a-c)

Add DOCS options to ports that should have one.

Also various fixes related to said option.

PR:		230864
Submitted by:	mat
exp-runs by:	antoine

update ports:
	biology/phrab
	biology/phred
	biology/consed

Although these programs are licensed freely for academic and nonprofit
purposes, users have to contact the authors to obtain the tarballs.

PR:		191336
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)

Replace maintainer's email address with one that seems to work

With hat:	portmgr

Convert biology to MDOCS and MEXAMPLES

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

- Get Rid MD5 support

Teach the building cluster that these ports are not to be build

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>

16 vulnerabilities affecting 89 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities

Last updated:
2020-05-31 11:54:41