Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

By Robert Schmieder, Robert A. Edwards. PLoS ONE, 2011

720 citations recorded by the source corpus.

High-throughput sequencing technologies have strongly impacted microbiology, providing a rapid and cost-effective way of generating draft genomes and exploring microbial diversity. However, sequences obtained from impure nucleic acid preparations may contain DNA from sources other than the sample. Those sequence contaminations are a serious concern to the quality of the data used for downstream analysis, causing misassembly of sequence contigs and erroneous conclusions. Therefore, the removal of sequence contaminants is a necessary and required step for all sequencing projects. We developed DeconSeq, a robust framework for the rapid, automated identification and removal of sequence contamination in longer-read datasets (150 bp mean read length). DeconSeq is publicly available as standalone and web-based versions. The results can be exported for subsequent analysis, and the databases used for the web-based version are automatically updated on a regular basis. DeconSeq categorizes possible contamination sequences, eliminates redundant hits with higher similarity to non-contaminant genomes, and provides graphical visualizations of the alignment results and classifications. Using DeconSeq, we conducted an analysis of possible human DNA contamination in 202 previously published microbial and viral metagenomes and found possible contamination in 145 (72%) metagenomes with as high as 64% contaminating sequences. This new framework allows scientists to automatically detect and efficiently remove unwanted sequence contamination from their datasets while eliminating critical limitations of current methods. DeconSeq's web interface is simple and user-friendly. The standalone version allows offline analysis and integration into existing data processing pipelines. DeconSeq's results reveal whether the sequencing experiment has succeeded, whether the correct sample was sequenced, and whether the sample contains any sequence contamination from DNA preparation or host. In addition, the analysis of 202 metagenomes demonstrated significant contamination of the non-human associated metagenomes, suggesting that this method is appropriate for screening all metagenomes. DeconSeq is available at http://deconseq.sourceforge.net/.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/15bb08a32a3aba97e7b691bebf898ed576ea4444

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Citations in the corpus

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis (2013, methodology): “All trimming tools were run on GNU/Linux machines at varying Q thresholds (single Q for most, with Qleft = Qright for PRINSEQ, combinations of HQ and LQ for ConDeTri).”
ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. (2017, background): “DeconSeq [8] requires a pre-built database of potential contaminants that is specialized to detect human DNA in genome or metagenome assemblies.”
Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery (2017, positive): “To remove human contamination, high quality reads were mapped to the human genome (GRCh38) using DeconSeq (v 0.4.3) and highly similar sequences to the human genome reference were subsequently removed from the dataset 64 .”