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The Comprehensive R Archive Network
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Our manuscript is currently under review. CiDD may be obtained by visiting cidd. SyQADA allows the simple specification of protocols that marshal and manage input data, allowing analyses to be run repeatably over large volumes of data for many samples and for different projects.
Use of SyQADA requires Unix, python3, and no other software besides a text editor and the analysis programs used in the workflow.
SyQADA exposes no programming interface. Configuration files are simple property lists; the protocol of a workflow is expressed as a list of task definitions and attributes. Analyses included the Affymetrix birdsuite, the gatk best practices variant calling workflow, hapLOH, hapLOHseq, Ion Reporter, JLOH, mach, mutect, pairwise phasing, the Tuxedo suite and varscan2 as well as numerous small programs for pre- and post-processing data.
SyQADA is coming soon at syqada. PolyAna Homopolymer Analyzer PolyAna was developed as a quality control step in processing of Ion Torrent sequencing data to identify and remove potential homopolymers from the detected somatic mutations.
The Ion semiconductor technology suffers from inaccurately estimating the number of nucleotides within the homopolymer regions and therefore results in false somatic mutation calls.