Phrap pipeline

Phrap specifications

Information


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

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Maintainer


  • person_outline Philip Green <>

Publication for Phrap

Phrap IN pipelines

 (7)
2016
PMCID: 5017806
PMID: 27431373
DOI: 10.1264/jsme2.ME16001

[…] by genomic dna. experiments were performed in triplicate (i.e., three test tubes per condition for each strain)., multiple reads obtained by sequencing reactions were assembled using the phred-phrap program (7). the nucleotide sequences of multiple clones were aligned using clustalw, and used to generate phylogenetic trees. phylogenetic trees were constructed based on the maximum […]

2014
PMCID: 4079543
PMID: 24847883
DOI: 10.1038/nature13377

[…] of functional metagenomic selections4. assembly with parfums consists of: (i) three iterations of variable job size with the short-read assembler velvet29, (ii) two iterations of assembly with phrap30, and (iii) custom scripts to clean sequence reads, remove chimeric assemblies, and link contigs by coverage and common annotation, as described4. in addition to outperforming traditional, […]

2013
PMCID: 4015439
PMID: 24144118
DOI: 10.1186/1471-2180-13-233

[…] 72°c for 10 min, pcr amplicons were similarly cloned into the pcr2.1-topo vector as described above. at least 10 independent clones from each reaction were sequenced, and all reads were assembled by phrap as described above. regions representing 18s, its1, 5.8s, its2 and partial 28s sequences were determined by rfam (http://rfam.janelia.org) [14]., the assembled o. petrowi 18s rrna sequence […]

2010
PMCID: 2854126
PMID: 20404998
DOI: 10.1371/journal.pntd.0000658

[…] and t. b. gambiense genome sequences are very similar in terms of content, gene order and sequence identity. the absence of potentially gambiense-specific sequences was confirmed by examining a phrap assembly of those capillary reads that did not map against the t. brucei 927 reference genome. analysis of ∼40,000 unmapped sequence reads using blastx showed that among them were features […]

2010
PMCID: 2872872
PMID: 20128909
DOI: 10.1186/gb-2010-11-2-r12

[…] into the ids of the plant repetitive sequences in the plant repeat database [30]., overlapping, non-cognate short reads generated by the gs-flx run were assembled using the 64 bit manyreads build of phrap ver 1.080721 [52]. all assemblies were done on a 16-core intel xeon 2.93 ghz server with 128gb ddr2 ram. parameters for the phrap assembly were the same as those used in [23], except […]

Phrap institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

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