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Phrap | Assembling genomic DNA sequences

Allows to compare, align, and assemble large sets of DNA sequences. PHRAP uses a banded version of the Smith-Waterman-Gotoh algorithm to do pairwise comparisons of the sequences. It compares sequences by searching for pairs of perfectly matching “words” or sequence regions that meet criteria, tries to extend the alignment if a match of the designated word size is found and then scores it. The software uses quality values produced by the PHRED basecaller. Cross match/Swat is included in the PHRAP package.

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Phrap forum

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Phrap classification

Phrap specifications

Unique identifier:
OMICS_01429
Interface:
Command line interface
Input data:
Sequence and quality files
Output data:
Standard error, contig sequences, contig qualities
Operating system:
Unix/Linux, Mac OS
Version:
0.990319
Requirements:
C compiler
Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTA
Output format:
FASTA
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

Phrap distribution

versioning

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Phrap support

Documentation

Maintainer

  • Philip Green <>

Credits

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Publications

Institution(s)

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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