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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>
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447 B
Text
8 lines
447 B
Text
Phred and consed write sequence and quality value information in
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'phd' output files. A phd file contains information in a header,
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the called bases, the base quality values, and the base call trace
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locations. Phd2fasta reads phd files and writes sequence and quality
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value FASTA files, which phrap and cross_match need as input.
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(Consed needs phd files in order to obtain the base call locations.)
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WWW: http://www.phrap.org/phredphrapconsed.html
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