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

SUBMITTER: Tennessen K 

PROVIDER: S-EPMC4681846 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature