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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
BOWTIE, gnuplot and Sun Grid Engine or TORQUE as cluster manager if running NGSQC on a LINUX cluster
Maintained No




No version available


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Publication for Next Generation Sequencing Quality Control

NGSQC citations


Draft Genome Sequence of Multidrug Resistant Escherichia coli NIVEDI P44, Isolated from a Chicken Fecal Sample in Northeast India

Genome Announc
PMCID: 5920187
PMID: 29700135
DOI: 10.1128/genomeA.00205-18
call_split See protocol

[…] eterinary medicine.The strain was sequenced using the Illumina HiSeq sequencing platform. The paired-end technology of Illumina platform produced a total of 12,884,022 paired-end reads of 100 bp. The next-generation sequencing quality control (NGS QC) toolkit version 2.3 () was used to filter high-quality data for the genome assembly. A total of 11,499,584 reads were generated and assembled using […]


Transcriptome of Porcine PBMCs over Two Generations Reveals Key Genes and Pathways Associated with Variable Antibody Responses post PRRSV Vaccination

Sci Rep
PMCID: 5802836
PMID: 29410429
DOI: 10.1038/s41598-018-20701-w

[…] Adaptor sequences, unknown sequences (N), low-quality reads (Q < 20), and their paired sequences measuring less than 50 bases were eliminated from raw reads using Next Generation Sequencing Quality Control Toolkit version 2.3.3.Reference genome and gene annotation files were downloaded from Ensembl ( A set of gen […]


Exploring Genomic Variants Related to Residual Feed Intake in Local and Commercial Chickens by Whole Genomic Resequencing

PMCID: 5852553
PMID: 29364149
DOI: 10.3390/genes9020057

[…] paired-end reads. Reads of extremely low quality (>10 consecutive nucleotides with Phred scores < 10), with adaptor contamination or without a quality control-passed paired read were discarded using NGSQC toolkit (v2.3.3), resulting in a qualified clean dataset. More than 20× coverages were determined for each pool (). All clean sequenced reads were mapped to a reference genome (Galgal 4.0) using […]


Regeneration of functional alveoli by adult human SOX9+ airway basal cell transplantation

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

[…] ality 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 exp […]


Absence of Correlation between Chimeric RNA and Aging

PMCID: 5748704
PMID: 29240691
DOI: 10.3390/genes8120386
call_split See protocol

[…] The Genotype-Tissue Expression (GTEx) raw RNA-Seq data was downloaded. Next Generation Sequencing Quality Control toolkit ( was used for filtering off low-quality reads. Paired end sequencing reads were mapped to Human genome ver […]


Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration

PMCID: 5704526
PMID: 29179682
DOI: 10.1186/s12876-017-0683-9

[…] nces shorter than 100 nucleotides, with any ambiguous nucleotide, or with an overlap of fewer than 20 nucleotides in paired reads were purged. The merged reads were subjected to quality control using NGSQC Toolkit [], to exclude those with average Phred quality score below 30. The selected high-quality reads were processed using Quantitative Insights into Microbial Ecology (QIIME V1.8) software pa […]


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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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