NGSQC protocols

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 No
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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Publication for Next Generation Sequencing Quality Control

NGSQC IN pipelines

PMCID: 5829276
PMID: 29344809
DOI: 10.1007/s13238-018-0506-y

[…] was verified by agilent 2100 bioanalyzer and real-time quantitative pcr. then the library is sequenced using illumina hiseq 4000. clean data were acquired from raw data (fastq format) using the ngsqc toolkit by removing low-quality reads. clean rna-seq reads were mapped to the reference genome (ensembl, grch37) using tophat v2.0.049 using default settings., with genome mapping result, gene […]

PMCID: 5024101
PMID: 27628568
DOI: 10.1038/srep33297

[…] as described26. the rna-seq data consisted of >350 million high-quality reads (supplementary table s1). the reads from each sample were filtered to remove adapters and low-quality reads using ngsqc tool kit45 followed by mapping on the chickpea (kabuli cdc frontier) genome19 using splice read aligner tophat229. the transcriptome of each tissue was assembled using cufflinks and merged […]

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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