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NGSQC | Cross-platform quality analysis pipeline for deep sequencing data

Provides a set of quality control measures to detect quality issues in deep sequencing data derived from 2D surfaces. NGSQC is a comprehensive deep sequencing quality control pipeline that can help biomedical researchers find out if there are specific quality issues related to their results. The software performs various analysis and reporting tasks in a pipeline. Users can take advantage of multiprocessor/core computers by specifying a number of jobs that can run simultaneously.

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NGSQC classification

NGSQC specifications

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

NGSQC distribution

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NGSQC support

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Credits

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Publications

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

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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