NGSQC specifications


Unique identifier OMICS_01064
Alternative name Next Generation Sequencing Quality Control
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Output data A file that organizes the quality measures in a three-layered hierarchical output.
Output format HTML
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.4
Stability Stable
Requirements BOWTIE, gnuplot and Sun Grid Engine or TORQUE as cluster manager if running NGSQC on a LINUX cluster
Maintained No



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NGSQC article

NGSQC citations

PMCID: 4758086

[…] hiseq 2000 platform was used to generate paired-end 100-bp raw reads for each enriched library according to the manufacturer’s protocol. quality filtering of the raw reads was performed using ngsqc tookit v2.3.3 [61]. for each sample, we discarded reads that did not have an overall quality score of 20 using the phred33 scale for at least 70 % of the bases or for any base with quality less […]

PMCID: 4583709

[…] million) and fpkm (fragments per kilobase per million). log to the base 2 of fpkm was considered as absolute expression or delta ct equivalent value., quality control of individual libraries using ngsqc tool kit revealed an average of 95.85% hq reads based on q20 score. total number of hq reads on an average per library was ~ 47 million, indicating significant amount of reads to proceed […]

NGSQC institution(s)
Department of Psychiatry and Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, USA; National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA
NGSQC funding source(s)
Supported by R01CA144043-01, a University of Michigan Center for Computational Medicine and Biology Pilot Project, the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. and partly by the National Center for Integrated Biomedical Informatics through NIH grant 1U54DA021519-01A1 to the University of Michigan.

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