title: acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.
abstract: BACKGROUND
  A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable quality control efforts are put into post-sequencing analysis. Contamination screening generally relies on reference-based methods such as database alignment or marker gene search, which limits the set of detectable contaminants to organisms with closely related reference species. As genomic coverage in the tree of life is highly fragmented, there is an urgent need for a reference-free methodology for contaminant identification in sequence data.
  
  
  RESULTS
  We present acdc, a tool specifically developed to aid the quality control process of genomic sequence data. By combining supervised and unsupervised methods, it reliably detects both known and de novo contaminants. First, 16S rRNA gene prediction and the inclusion of ultrafast exact alignment techniques allow sequence classification using existing knowledge from databases. Second, reference-free inspection is enabled by the use of state-of-the-art machine learning techniques that include fast, non-linear dimensionality reduction of oligonucleotide signatures and subsequent clustering algorithms that automatically estimate the number of clusters. The latter also enables the removal of any contaminant, yielding a clean sample. Furthermore, given the data complexity and the ill-posedness of clustering, acdc employs bootstrapping techniques to provide statistically profound confidence values. Tested on a large number of samples from diverse sequencing projects, our software is able to quickly and accurately identify contamination. Results are displayed in an interactive user interface. Acdc can be run from the web as well as a dedicated command line application, which allows easy integration into large sequencing project analysis workflows.
  
  
  CONCLUSIONS
  Acdc can reliably detect contamination in single-cell genome data. In addition to database-driven detection, it complements existing tools by its unsupervised techniques, which allow for the detection of de novo contaminants. Our contribution has the potential to drastically reduce the amount of resources put into these processes, particularly in the context of limited availability of reference species. As single-cell genome data continues to grow rapidly, acdc adds to the toolkit of crucial quality assurance tools.
authors.affiliation: Computational Methods for the Analysis of the Diversity and Dynamics of Genomes, Bielefeld University, Universitätsstr. 25, Bielefeld, 33615, Germany. mlux@techfak.uni-bielefeld.de.
authors.forename: Markus
authors.initials: M
authors.lastname: Lux
authors.affiliation: Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstr. 27, Bielefeld, 33615, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Krüger
authors.affiliation: Australian Centre for Ecogenomics, University of Queensland, ST LUCIA, Brisbane, QLD 4072, Australia.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.affiliation: Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstr. 27, Bielefeld, 33615, Germany.
authors.forename: Irena
authors.initials: I
authors.lastname: Maus
authors.affiliation: Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstr. 27, Bielefeld, 33615, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
authors.affiliation: , 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstr. 27, Bielefeld, 33615, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.affiliation: CITEC centre of excellence, Bielefeld University, Inspiration 1, Bielefeld, 33619, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Hammer
mesh_terms: D016000:Cluster Analysis; D004247:DNA / Q000032:analysis / Q000235:genetics; D059018:DNA Contamination; D016678:Genome; D000069550:Machine Learning; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D004247:DNA
keywords: Binning; Clustering; Contamination detection; Machine learning; Quality control; Single-cell sequencing