title: ProDeGe: a computational protocol for fully automated decontamination of genomes.
abstract: Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes--clean and contaminant--using a combination of homology and feature-based methodologies. On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). The procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Tennessen
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Andersen
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Clingenpeel
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.affiliation: Department of Biology and Curriculum in Genetics, University of North Carolina, Chapel Hill, NC, USA.
authors.forename: Derek S
authors.initials: DS
authors.lastname: Lundberg
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: James
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics, University of North Carolina, Chapel Hill, NC, USA.
authors.forename: Jeff L
authors.initials: JL
authors.lastname: Dangl
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.affiliation: Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D016678:Genome; D054892:Metagenome; D008969:Molecular Sequence Data; D012689:Sequence Homology, Nucleic Acid