Phred pipeline

Phred specifications


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


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  • person_outline Phil Green <>

Publications for Phred

Phred IN pipelines

PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] read processing and mapping was carried out with the clc genomics workbench (qiagen aarhus a/s). reads were trimmed by removing adapter sequences using the trim sequences tool and filtered for phred quality scores <30 [40]. reads from primary transcriptome libraries containing the barcode sequence taccctag at their 5′-ends indicated a false positive tss and were removed from the read […]

PMCID: 5300976
PMID: 28239369
DOI: 10.3389/fmicb.2017.00172

[…] light, until injection of samples in a megabace 1000tm sequencer (amersham biosciences, usa)., the contigs were assembled using the forward and reverse sequences of each 16s rrna gene amplicon using phred (ewing and green, 1998; ewing et al., 1998). the dna sequences were analyzed utilizing the blastn program (altschul et al., 1997). the sequences were aligned using the program muscle (edgar, […]

PMCID: 5576253
PMID: 28851277
DOI: 10.1186/s12864-017-4080-0

[…] attempted to gain information on ranges of these mt-mrnas by approximating their 5′ ends using the rna-seq data., the rna-seq reads were subjected to the trimming of low-quality (less than 10 in the phred quality score; [31]) and short (less than 20 bp) reads with solexaqa [32]. the in-house blastn search (e-value cutoff: 1e-5) was then conducted with the mtdna sequence of an rna-sequenced […]

PMCID: 5716196
PMID: 29036322
DOI: 10.1093/nar/gkx853

[…] internal restriction sites of nspi or bfuci. only reads with the correct barcodes and re sites were retained for further processing. retained reads were subjected to quality trimming. bases with phred quality value <15 (out of 40) (21,22), i.e. error rates of ≤3%, were further removed with another custom perl script. each read was examined in two phases. in the first phase reads […]

PMCID: 5736867
PMID: 29326752
DOI: 10.3389/fgene.2017.00213

[…] the adaptor sequence from the 3′ ends and all reads without detectable adaptor sequences were removed from the dataset. next the length distribution and the base call accuracy, represented by the phred quality scores (q score), were calculated using the quality control software fastqc (babraham bioinformatics, uk, version 0.10.1). in order to prevent bias and false-positive mapping […]

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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