PIQA protocols

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PIQA specifications


Unique identifier OMICS_01067
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format HTML report
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability No
Maintained No


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Publication for PIQA

PIQA in pipeline

PMCID: 5143363
PMID: 28018607
DOI: 10.1038/hgv.2016.41

[…] to hybridize and capture the dna fragments. after hybridization, the captured dna was sequenced on illumina hiseq2500 analyzers (illumina, sandiego, ca, usa) and read on quality analysis pipeline (piqa). we used bwa v0.59 to align the sequence reads to the human genome reference (build 37) and removed duplicated reads from the subsequent analyses. sequences variants were identified […]

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PIQA in publications

PMCID: 5412055
PMID: 28464870
DOI: 10.1186/s12864-017-3699-1

[…] hiseq2000 platform in pe mode agrf, giving between 17 and 33 million pairs of reads per sample., for each venturia isolate, a quality check (qc) on genome sequencing data was carried out utilising piqa v1.0 [], the fastx toolkit v0.0.13 [] and fastqc []. reads were trimmed using in-house perl tools and adaptor sequences were removed using fastq-mcf [] based on data qc reports. de novo genome […]

PMCID: 3956068
PMID: 23341494
DOI: 10.1093/bib/bbs086

[…] processing and visualization functionality. in addition, software tools have been published that support only the illumina platform (i.e. fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit), piqa [] and tileqc []) or provide certain specialized functionality (i.e. tagcleaner [])., after reads have been processed to meet a certain quality standard, they are usually aligned to an existing […]

PMCID: 3466296
PMID: 23056439
DOI: 10.1371/journal.pone.0046759

[…] processed the reads with the illumina ga pipeline 1.4. all reads were single-end reads, regardless of their length. we used firecrest for image processing and bustard for base calling. we used the piqa pipeline to assess the quality of the reads and determined that the sequencing quality declined after 31 bps. therefore, we trimmed all the reads, regardless of their initial length to a length […]

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PIQA institution(s)
Department of Computer Science, University of Houston, Houston, TX, USA; Department of Physics, Universidad de Guadalajara, Jalisco, México; Eureka Genomics Corp; Houston, TX, USA
PIQA funding source(s)
Department of Homeland Security Science and Technology Directorate (award NBCHC070063); Texas Learning and Computation Center; training fellowship from the Keck Center Biomedical Discovery Training Program of the Gulf Coast Consortia (NIH Grant No. 1 T90 DA022885-02); CONACYT, Mexico for scholarship support

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