bcbio-nextgen is an Python framework for next generation sequencing analysis. The fully automated pipeline interacts with the sequencing machine, runs sequences through configurable processing pipelines, and uploads the data into Galaxy for visualization and additional processing. The variant calling analysis pipeline handles alignment to a reference genome, variant identification with GATK and preparation of summary PDF files for assessing run quality.
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Roman Valls Guimerà (2012) studied this question.