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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>
22 lines
1.2 KiB
Plaintext
22 lines
1.2 KiB
Plaintext
Phrap is a program for assembling shotgun DNA sequence data.
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Among other features, it allows use of the entire read and not just the
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trimmed high quality part, it uses a combination of user-supplied and
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internally computed data quality information to improve assembly accuracy
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in the presence of repeats, it constructs the contig sequence as a mosaic
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of the highest quality read segments rather than a consensus, it provides
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extensive assembly information to assist in trouble-shooting assembly
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problems, and it handles large datasets.
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This package also contains Swat and Cross_match.
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Swat is a program for searching one or more DNA or protein query sequences
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against a sequence database, using (an efficient implementation of) the
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Smith-Waterman-Gotoh algorithm.
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Cross_Match is a general-purpose utility based on Swat for comparing any
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two sets of DNA sequences, and it can be used to:
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* produce vector-masked versions of a set of reads
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* compare a set of cDNA sequences to a set of cosmids
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* compare contigs found by two altanative assembly procedures to each other
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* compare phrap contigs to the final edited cosmid sequence.
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WWW: http://www.phrap.org/phredphrapconsed.html
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