NGS QC Toolkit pipeline

NGS QC Toolkit specifications


Unique identifier OMICS_01062
Name NGS QC Toolkit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format FASTQ, HTML report, tab-delimited text
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.3.3
Stability Stable
Maintained Yes


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  • person_outline Mukesh Jain <>

Publication for NGS QC Toolkit

NGS QC Toolkit citations

PMCID: 5809551

[…] libraries, led to the use of a de novo transcriptome assembly pipeline. at first, raw rna-seq data were trimmed from adaptors and sequencing artefacts, as well as low quality fragments, using the ngs qc toolkit. the high-quality reads obtained were then subjected to in silico normalization prior to de novo assembly to reduce the sequencing coverage of highly represented regions […]

PMCID: 5804362

[…] sequenced on illuminahiseq 4000 platform with paired-end 150 base pair long reads. clean data were obtained from raw data by removing reads containing adapter, n base, and low-quality reads with ngs qc toolkit (version: 2.3.3). clean data were mapped to the reference genome of r.norvegicus6.0 and estimated for gene expression level using tophat2 and cufflinks (version: 2.2.1)., osgin1, […]

PMCID: 5623955

[…] hiseq x ten (read length, pe150, 13 independent samples) platforms. all raw sequence data have been deposited in the ncbi sequence read archive (sra, accession number srp069764)., we used the ngs qc toolkit v2.3.3 software to filter the reads with adapter sequences, reads with an unknown base (n, unknown bases in a read > 5%), and low-quality reads (reads with base quality ≤ 20). […]

PMCID: 5605536

[…] default parameters (minimum probability for a read to contain zero errors = 75%, minimum average phred score for a sequence read = 20, and minimum phred score for each base of a read = 10) using ngs qc toolkit60. for improving the quality of de novo assembly, filtered reads from in-house transcriptome data (unpublished) for young unopened floral bud and full bloomed flower tissues were also […]

PMCID: 5577132

[…] sample prep kit (illumina), and 2 × 100 bp paired-end reads were sequenced by the illumina hiseq. 2000 protocols (bgi, shenzhen, china). we obtained abundant clean data. after filtering with ngs qc toolkit (v2.3)30 with default parameters, 191.1 × 106, 187.5 × 106, and 354.9 × 106 high quality read pairs were obtained from rumpless males, normal males, and rumpless females, […]

NGS QC Toolkit institution(s)
Functional Genomics and Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India

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