Phrap protocols

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Phrap specifications


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
C compiler
Maintained Yes



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  • person_outline Philip Green <>

Publication for Phrap

Phrap in pipelines

PMCID: 5798811
PMID: 29423233
DOI: 10.1038/s41438-017-0002-1

[…] the detailed parameters for blastn were: blastn –db database_name –query input_file –out output_file –evalue 1e-5 –word_size 9 –outfmt 6., default parameters were used for amos, minimus, and phrap. connected contigs were linked, and the gaps were filled by blastn and pcr experiments. the whole-genome sequence was corrected based on illumina sequencing data using bwa software., a novel […]

PMCID: 5281586
PMID: 28197131
DOI: 10.3389/fmicb.2017.00061

[…] edited using bioedit software and aligned with clustal x. for the construction of the dendrogram, sequences were checked for quality, aligned and analyzed using the software phred v.0.20425 (), phrap v.0.900319 () and consed 12.0 (). the phylogenetic tree was developed using the neighbor-joining method present in mega version 5.0 (). genetic distance was calculated based on kimura […]

PMCID: 5327432
PMID: 28240222
DOI: 10.1038/srep43200

[…] reads were used again for gap filling of scaffolds, then gap-filled scaffolds were clustered to remove redundant sequences using the tgicl tool, and overlapped scaffolds were further assembled using phrap assembly ( to obtain sequences that had the least ns and could not be extended on either end. such sequences are defined as unigenes. the following parameters were used […]

PMCID: 5399367
PMID: 28429786
DOI: 10.1038/srep46490

[…] exons and splicing regions of slc10a1 for 40 unrelated pi samples (). each fragment amplified by pcr from genomic dna was sequenced on both strands with an abi prism 3700 sequencer. the phred-phrap-consed-polyphred package ( was used to assemble the sequences and identify variants., to test for differentiation between populations, three measures […]

PMCID: 5496344
PMID: 28676050
DOI: 10.1186/s12918-017-0441-1

[…] without mapped 454 reads; the second set of data was constructed using 454 reads that had a hit against illumina contigs and the corresponding illumina reads. this data was reassembled using the phrap1 software. the third dataset corresponds to the transcripts assembled by wgs-assembler, using 454 reads that did not have hits against illumina transcripts. transcripts from these three sets […]

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Phrap in publications

PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] amylovorus jbd401 (kctc 11515bp) genome was sequenced by next-generation sequencing using 454 (454 gs flx) and illumina methods. initially, 454 dna reads were assembled into contigs with the phred/phrap/consed [] software package and subcontracted to macrogen inc. further contigs were assembled using geneious pro.5.5 software [] and clc workbench software (clc bio-qiagen). mapping of assembled […]

PMCID: 5907745
PMID: 29673385
DOI: 10.1186/s13071-018-2839-z

[…] ment}$$ \mathrm{p}\left(\mathrm{hrf}\cap \mathrm{hra}\right)\mid {p}^{+}=\mathrm{p}\left(\mathrm{hrf}|{p}^{+}\right)\ast \mathrm{p}\left(\mathrm{hra}|{p}^{+}\right) $$\end{document}phrf∩hra∣p+=phrfp+∗phrap+ 4\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \use […]

PMCID: 5902291
PMID: 29620669
DOI: 10.1097/MD.0000000000009545

[…] foster city, ca, usa). a sequence of 34 bases downstream of the gp5+ binding site was used for accurate genotyping of hpv types.[] the generated sequences were quality assessed by use of phred/phrap/consed software and were then aligned and checked for similarity with the sequences deposited in genbank using the blast tool - basic local alignment system,[] bioedit – biological sequence […]

PMCID: 5858127
PMID: 29560044
DOI: 10.1186/s13100-018-0115-6

[…] indicate an insertion that was only present in the genome of the olive baboon., our papio specific set of alu elements was aligned to the aluy consensus sequence [] using cross_match (; last accessed december 2017). the data set was then analyzed via coseg (; last accessed november 2017) to determine […]

PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] shredded into 1.5 kb overlapping shreds. the 454 newbler consensus shreds were integrated, the illumina velvet consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version sps – 4.24 (high performance software, llc). the software consed (ewing et al., ; ewing and green, ; gordon et al., ) was used in the following finishing process. illumina data […]

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

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