NGS-Bits specifications


Unique identifier OMICS_20169
Name NGS-Bits
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, VCF, BED, FASTQ
Output format qcML, TSV, SAM, BAM, VCF, BED, FASTQ, FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.1
Stability Stable
g++, qmake, git, cmake, python, matplotlib
Maintained Yes


  • MappingQC
  • ReadQC
  • SomaticQC
  • VariantQC




No version available


  • person_outline Christopher Schroeder

Publication for NGS-Bits

NGS-Bits citations


Transcriptomic profiling of purified patient derived dopamine neurons identifies convergent perturbations and therapeutics for Parkinson’s disease

Hum Mol Genet
PMCID: 5409122
PMID: 28096185
DOI: 10.1093/hmg/ddw412

[…] By checking the quality of RNA sequencing data using the FASTQC software (version 0.9.3) ( via the CGAT pipeline, we observed (i) an abnormal GC content and per base GC content for 5’ reads due to Hexamer priming bias () () and (ii) an overrepresentation of some RNA sequence due to adapter contaminatio […]


High fat diet disrupts metabolism in two generations of rats in a parent of origin specific manner

Sci Rep
PMCID: 4994008
PMID: 27550193
DOI: 10.1038/srep31857
call_split See protocol

[…] matic pipeline (). All raw RNA-seq data, and processed count tables are archived at the Gene Expression Omnibus with accession number GSE80721. The code used to perform read quality control ( and short read alignment ( can be found at […]

NGS-Bits institution(s)
Institute of Medical Genetics and Applied Genomics, University of Tubingen, Tubingen, Germany; Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Tubingen, Germany; Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Tubingen, Germany; Department of Internal Medicine I, University Hospital Tubingen, Tubingen, Germany
NGS-Bits funding source(s)
Supported by the Federal Ministry of Education and Research (BMBF) [FKZ 01ZX1301A].

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