title: NGSQC: cross-platform quality analysis pipeline for deep sequencing data.
abstract: BACKGROUND
  While the accuracy and precision of deep sequencing data is significantly better than those obtained by the earlier generation of hybridization-based high throughput technologies, the digital nature of deep sequencing output often leads to unwarranted confidence in their reliability.
  
  
  RESULTS
  The NGSQC (Next Generation Sequencing Quality Control) pipeline provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues.
  
  
  CONCLUSIONS
  Next generation sequencing platforms have their own share of quality issues and there can be significant lab-to-lab, batch-to-batch and even within chip/slide variations. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequence alterations, are not caused by low quality sequencing.
authors.affiliation: Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA. daimh@umich.edu
authors.forename: Manhong
authors.initials: M
authors.lastname: Dai
authors.forename: Robert C
authors.initials: RC
authors.lastname: Thompson
authors.forename: Christopher
authors.initials: C
authors.lastname: Maher
authors.forename: Rafael
authors.initials: R
authors.lastname: Contreras-Galindo
authors.forename: Mark H
authors.initials: MH
authors.lastname: Kaplan
authors.forename: David M
authors.initials: DM
authors.lastname: Markovitz
authors.forename: Gil
authors.initials: G
authors.lastname: Omenn
authors.forename: Fan
authors.initials: F
authors.lastname: Meng
mesh_terms: D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface