PIQA

Application data
Principal bioinformatics method(s)	Sequencing quality control
Technology	Illumina
Maintained?	Maybe
Input format(s)	bustard, FASTQ, scarf
Programming language(s)	R

Summary: PIQA is a quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). It is a set of libraries for R.

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Produces a bunch of report files and graphics describing run quality. The paper cited describes a base quality score range of -40 to 40, which doesn't seem to correspond to old/new Illumina pipelines or Sanger fastq quality scores. Note that PIQA will not process fastq files using Sanger quality scores.