Abstract
With the rapid growth and development of sequencing technologies, genomes have become the new go-to for exploring solutions to some of the world’s biggest challenges such as searching for alternative energy sources and exploration of genomic dark matter. However, progress in sequencing has been accompanied by its share of errors that can occur during template or library preparation, sequencing, imaging or data analysis. In this study we screened over 18,000 publicly available microbial isolate genome sequences in the Integrated Microbial Genomes database and identified more than 1000 genomes that are contaminated with PhiX, a control frequently used during Illumina sequencing runs. Approximately 10% of these genomes have been published in literature and 129 contaminated genomes were sequenced under the Human Microbiome Project. Raw sequence reads are prone to contamination from various sources and are usually eliminated during downstream quality control steps. Detection of PhiX contaminated genomes indicates a lapse in either the application or effectiveness of proper quality control measures. The presence of PhiX contamination in several publicly available isolate genomes can result in additional errors when such data are used in comparative genomics analyses. Such contamination of public databases have far-reaching consequences in the form of erroneous data interpretation and analyses, and necessitates better measures to proofread raw sequences before releasing them to the broader scientific community.
Highlights
The ability to produce large numbers of high-quality, low-cost reads has revolutionized the field of microbiology [1,2,3]
We identify and catalog more than 1000 genomes in public databases (i.e. Genbank) that are contaminated with PhiX sequences and the approximately 10% of the genomes that are published in literature
Among the isolate bacterial and archaeal genomes in Integrated Microbial Genomes (IMG) v4.0, 1230 scaffolds from 1041 genomes were contaminated with PhiX sequences, with 105 contaminated genomes published in literature (Additional files 1 and 2)
Summary
The ability to produce large numbers of high-quality, low-cost reads has revolutionized the field of microbiology [1,2,3]. As of November 17th 2014, there were 41,553 bacterial and archaeal isolate genome sequencing projects reported in GOLD [4,5] This explosion of genome sequencing projects especially during the last 5 years has been largely catalyzed by the development of several next-generation sequencing platforms offering rapid and accurate genome information at a low cost. The Illumina sequencing platform does come with its share of challenges [8] that need to be addressed by the users of this technology. One such challenge is the protocol in which PhiX is used as a quality and calibration control for sequencing runs. Addition of PhiX as a sequencing control necessitates subsequent quality control steps to remove the sequences such that they do not get integrated as part of the target genome
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