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

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Versioning


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Maintainer


  • person_outline Christopher Schroeder <>

Publication for NGS-Bits

NGS-Bits in publications

 (3)
PMCID: 5409122
PMID: 28096185
DOI: 10.1093/hmg/ddw412

[…] 2000 system., 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 […]

PMCID: 4994008
PMID: 27550193
DOI: 10.1038/srep31857

[…] 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., variance stabilising transformed (vst) read counts for protein-coding genes, […]

PMCID: 5003782
PMID: 26657142
DOI: 10.1038/nm.4002

[…] non-m characters in the cigar string. we discarded bam files if excessive numbers of indel carrying reads (≥20%) were detected (). the bam qc script has been deposited at https://github.com/ding-lab/variantqc and will be merged with pindel-c later., we simulated illumina sequence data containing complex indels of craig venter’s genome to test pindel-c, gatk, and varscan for detection […]


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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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