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|Interface||Command line interface|
|Restrictions to use||None|
|Output format||HTML report|
|Operating system||Unix/Linux, Mac OS, Windows|
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Publication for PIQA
Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range
[…] 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 as […]
Novel WISP3 mutations causing progressive pseudorheumatoid dysplasia in two Chinese families
[…] ed 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 by compariso […]
A survey of tools for variant analysis of next generation genome sequencing data
[…] ent, 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 ). […]
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