NGS-Bits statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool NGS-Bits
info

Tool usage distribution map

This map represents all the scientific publications referring to NGS-Bits per scientific context
info info

Associated diseases

info

Popular tool citations

chevron_left Read quality control Alignment evaluation File format conversion Bioinformatics workflows File merging Duplicate read removal File filtering File sampling File comparison File intersection File parsing-extraction File sorting chevron_right
Want to access the full stats & trends on this tool?

Protocols

NGS-Bits specifications

Information


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
Requirements
g++, qmake, git, cmake, python, matplotlib
Maintained Yes

Subtools


  • MappingQC
  • ReadQC
  • SomaticQC
  • VariantQC

Download


download.png
download.png
github.png

Versioning


No version available

Maintainer


  • person_outline Christopher Schroeder

Publication for NGS-Bits

NGS-Bits citations

 (2)
library_books

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

2017
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) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) via the CGAT pipeline pipeline_readqc.py, 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 […]

call_split

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

2016
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 (pipeline_readqc.py) and short read alignment (pipeline_mapping.py) can be found at https://github.com/CGATOxford/CGATPipelines. […]


Want to access the full list of citations?
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].

NGS-Bits reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review NGS-Bits