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NGS-QC Generator

A computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile.

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2 user reviews

2 user reviews

Gary Yung-Chih Lai's avatar image

Gary Yung-Chih Lai

It’s a very user-friendly (Galaxy-based) and helpful tool to test the quality of my ChIP-Seq datasets. Furthermore, the authors kindly helped to add a chicken reference genome not in their server before and continuously updated the tool’s functions after the paper has been published. For a beginner, I only suggest one thing to keep in mind: the publicly datasets the authors collected are mixed with different species, antibodies, and reads produced by different NGS platforms (e.g. Illumina GAII and HiSeq 2000). Based on my experience, the chicken with a smaller genome (~ 1.2GB), H3K27ac ChIP-Seq (strong histone modification antibody), and reads produced by Illumina HiSeq are easier to get a higher score compared to the mouse with a larger genome (~2.5 GB), p300 ChIP-Seq (weak transcription co-factor antibody, indirect binding DNA), and reads produced by GAII.

marco A. Mendoza's avatar image

marco A. Mendoza

The major characteristics of this approach is its universality; i.e. its capacity of assessing QC descriptors for any kind of ChIP-seq and enrichment-related datasets. In fact all other currently available methods require either the use of peak callers for sites annotations (which require different conditions when treating broad or sharp profiles) or they are mainly designed for sharp enrichment patterns. Importantly, the NGS-QC Generator tool has been used for assessing QC indicators for more than 7000 publicly available datasets and is expected to cover all available datasets in a close future. Such QC indicators are available through the dedicated website www.ngs-qc.org

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NGS-QC Generator classification

NGS-QC Generator specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

NGS-QC Generator distribution

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No versioning.

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Publications

Institution(s)

Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, Illkirch, France

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