NGS QC Toolkit protocols

NGS QC Toolkit computational protocol

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 IN pipelines

PMCID: 5809551
PMID: 29434251
DOI: 10.1038/s41598-018-21225-z

[…] 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: 5860705
PMID: 29558483
DOI: 10.1371/journal.pone.0194282

[…] (illumina, usa). reference genome sequence of pig (sscrofa 11.1) was downloaded from ensembl ( the raw sequencing reads was filtered by ngs qc toolkit with default parameters [21]. clean reads were mapped to the pig reference genome sequence using the burrows-wheeler alignment software with default parameters [22]. samtools was used […]

PMCID: 5899093
PMID: 29654251
DOI: 10.1038/s41598-018-24341-y

[…] and the sequencing kit was truseq sbs kit v3-hs. more than 40 million reads were generated for each sample. raw reads were filtered and trimmed by using the illuqc and trimmingreads tools of the ngs qc toolkit package45. the filtering process was carried out with the default options. the trimming was carried out with mild thresholds namely -q 5 -n 25. alignment has been done by using tophat2 […]

PMCID: 5946031
PMID: 29780373
DOI: 10.3389/fmicb.2018.00863

[…] base calling were conducted by the hiseq control software (hcs) + olb + gapipeline-1.6 (illumina, ca, united states) on the hiseq instrument., the raw mrna sequence reads were pre-processed using a ngs qc toolkit (v. 2.3) to remove low-quality bases with quality scores < 30 and adapter sequences (patel and jain, 2012). for paired-end illumina reads, both pairs were removed if either pair […]

PMCID: 5307762
PMID: 28193207
DOI: 10.1186/s12896-017-0337-6

[…] four 90-nt paired-end rna-seq libraries were generated at beijing genomics institute (bgi, shenzhen, china) with the hiseqâ„¢ 2000 platform. quality control of sequencing reads was performed with the ngs qc toolkit (version 2.3.3) [22], and the obtained high-quality reads were aligned to the e. coli atcc#8739 genome (genbank cp000946.1) with bowtie 2 (version 2.2.5) [23]. the aligned reads stored […]

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

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