NGS-QCbox specifications


Unique identifier OMICS_12194
Name NGS-QCbox
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Biological technology Illumina
Operating system Unix/Linux
Parallelization OpenMP
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Java, bash, Python, NGS-QCBox, Raspberry
Source code URL
Maintained Yes


No version available



  • person_outline Rajeev K. Varshney

Publication for NGS-QCbox

NGS-QCbox citations


QTL‐seq for rapid identification of candidate genes for 100‐seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea

Plant Biotechnol J
PMCID: 5095801
PMID: 27107184
DOI: 10.1111/pbi.12567

[…] The statistics of generated sequencing reads was estimated using raspberry tool of NGS‐QCbox (Katta et al., ). Further, QTL‐seq pipeline (, developed by Iwate Biotechnology Research Center, Japan) was used for calculating SNP […]


First‐generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations

Plant Biotechnol J
PMCID: 5066660
PMID: 26821983
DOI: 10.1111/pbi.12528
call_split See protocol

[…] le). Initially, duplicate reads were removed, further low‐quality reads (having phred score <30) and sequences shorter than 100 nucleotides, or containing ‘N’, were removed using in‐house QC pipeline NGS‐QCbox (Katta et al., ). After cleaning steps, filtered reads were mapped onto the reference genome with bowtie2 v2.2.4 (Langmead and Salzberg, ) using default options. Reads mapped on more than on […]

NGS-QCbox institution(s)
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western Australia, Crawley, Australia
NGS-QCbox funding source(s)
Authors are thankful to the CGIAR Generation Challenge Program for financial support.

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