Phred protocols

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Phred specifications

Information


Unique identifier OMICS_01809
Name Phred
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Sequence traces, chromatogram files
Input format SCF, ABI
Output format SCF, FASTA, XPAB, PHD
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • Cross_match
  • Swat

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Versioning


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Maintainer


  • person_outline Phil Green <>

Publications for Phred

Phred in pipelines

 (23)
2016
PMCID: 4710996
PMID: 26757703
DOI: 10.1186/s40168-015-0146-x

[…] soil (srx119222)., for each sequence, low quality segments (phred score <15 []) were trimmed using an in-house script and reads <50 bp discarded. next adaptor contaminants were filtered using cross-match (http://www.phrap.org) with parameters minmatch = 10 and minscore = 20. in addition, due to the large number of low quality reads in the permafrost sample, we applied an in-house script […]

2016
PMCID: 5172430
PMID: 15629042
DOI: 10.1016/S1672-0229(04)02006-6

[…] yield ests. the libraries were not normalized in order to preserve the random nature of the original expression patterns for quantitative analysis. we used the phred program for base calling (, ), cross_match for vector sequences masking, and phrap for sequence assembly. in this study we collected a total number of 4,687 est sequences after quality assessment and trimmed at q20 (phred […]

2016
PMCID: 5209427
PMID: 27844108
DOI: 10.1007/s00248-016-0885-7

[…] using the “ssaha2” package []. this package identifies regions of high similarity using the ssaha searching algorithm and aligns these by implementing cross-match sequence alignment [] based on the banded smith-waterman-gotoh algorithm []. for a hit to be retained, an alignment score equal to half of the read (at least) was required. the risk […]

2015
PMCID: 4319844
PMID: 25659089
DOI: 10.1371/journal.pone.0117188

[…] jz818318-jz818449). phred scores were used to assess the sequence quality and to remove low-quality regions (end clipping) [,], with the window length set to 100 and the standard quality to 20. the cross_match utility was used to remove irrelevant vector and e. coli dna sequences (http://www.phrap.com). ests that shared an identity of >95 out of 100 nucleotides were assembled in contiguous […]

2014
PMCID: 4323066
PMID: 25534935
DOI: 10.1093/jhered/esu079

[…] (applied biosystems). amplified fragments were sequenced in the forward and reverse complementary directions and a consensus sequence was created using a modified version of the phred (; ) and phrap/cross_match/swat () software (perl scripts provided by the nerc biomolecular facilty, uk). sequences that did not form a consensus between their forward or reverse strands, but that were of good […]


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Phred in publications

 (78)
PMCID: 5292376
PMID: 28239610
DOI: 10.1155/2017/9604762

[…] of the raw est data, the low-quality, adapter, and the vector sequences were removed with phred software [, ] (codoncode corp., dedham, ma). the remaining est sequences were reprocessed by using “cross-match” program which is application of phrap for the vector sequence trimming [, ]., prenatal and postnatal period est sequences were assembled separately into contigs with contig assembly […]

PMCID: 5172415
PMID: 15626331
DOI: 10.1016/S1672-0229(03)01005-2

[…] to yield ests. the libraries were not normalized in order to preserve the random nature of the original expression patterns for quantitative analysis. we used the phred program for base calling , cross_match for vector sequences masking, and phrap for sequence assembly. to do library clone duplication check we ran self sequence comparison within each library using blastn, and grouped […]

PMCID: 5117676
PMID: 27871234
DOI: 10.1186/s12864-016-3302-1

[…] (bgi), china. base calling of abi trace files was conducted using phred software []. the bases with phred quality score < 20 were trimmed, and the vector sequences were subsequently removed using cross_match []. after filtering out the sequences with a length shorter than 100 bp, the organellar dna sequences were removed by comparing the bess with the arabidopsis mitochondrial genome […]

PMCID: 5209427
PMID: 27844108
DOI: 10.1007/s00248-016-0885-7

[…] using the “ssaha2” package []. this package identifies regions of high similarity using the ssaha searching algorithm and aligns these by implementing cross-match sequence alignment [] based on the banded smith-waterman-gotoh algorithm []. for a hit to be retained, an alignment score equal to half of the read (at least) was required. the risk […]

PMCID: 4710996
PMID: 26757703
DOI: 10.1186/s40168-015-0146-x

[…] soil (srx119222)., for each sequence, low quality segments (phred score <15 []) were trimmed using an in-house script and reads <50 bp discarded. next adaptor contaminants were filtered using cross-match (http://www.phrap.org) with parameters minmatch = 10 and minscore = 20. in addition, due to the large number of low quality reads in the permafrost sample, we applied an in-house script […]


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Phred institution(s)
Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA
Phred funding source(s)
This tool was funded by the National Human Genome Research Institute.

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