Genome Project Standards in a New Era of Sequencing

By P. Chain, D. Grafham, Robert S. Fulton, Michael G. Fitzgerald, J. Hostetler, D. Muzny, Johar Ali, Bruce W. Birren, D. Bruce, C. Buhay and 35 more. Science, 2009

438 citations recorded by the source corpus.

More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data. For over a decade, genome sequences have adhered to only two standards that are relied on for purposes of sequence analysis by interested third parties (1, 2). However, ongoing developments in revolutionary sequencing technologies have resulted in a redefinition of traditional whole-genome sequencing that requires reevaluation of such standards. With commercially available 454 pyrosequencing (followed by Illumina, SOLiD, and now Helicos), there has been an explosion of genomes sequenced under the moniker “draft”; however, these can be very poor quality genomes (due to inherent errors in the sequencing technologies, and the inability of assembly programs to fully address these errors). Further, one can only infer that such draft genomes may be of poor quality by navigating through the databases to find the number and type of reads deposited in sequence trace repositories (and not all genomes have this available), or to identify the number of contigs or genome fragments deposited to the database. The difficulty in assessing the quality of such deposited genomes has created some havoc for genome analysis pipelines and has contributed to many wasted hours. Exponential leaps in raw sequencing capability and greatly reduced prices have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The result is an ever-widening gap between drafted and finished genomes that only promises to continue (see the figure, page 236); hence, there is an urgent need to distinguish good from poor data sets.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/48e8c2d7f089283139b440fe4bc0785ee991cb57

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Citations in the corpus

Insights from 20 years of bacterial genome sequencing (2015, background): “A set of standards for the quality of submitted genomes has been published previously (Chain et al. 2009).”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, methodology): “Progress is being made to create standardized protocols (Field et al., 2008; Chain et al., 2009; Gilbert, 2015; Droege et al., 2016).”
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (2014, methodology): “Of these 238 unique MGS genomes—including 181 new genomes from previously unsequenced species—met the Human Microbiome Project high-quality draft genome standard ( Supplementary Figs.”
Locating rearrangement events in a phylogeny based on highly fragmented assemblies (2016, background): “ca Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, K1N 6N5 Ottawa, Canada with no direct information on how to order the scaffolds with respect to each other [1].”
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data (2013, methodology): “For this demonstration, we chose an ~175-kb BAC (VMRC53-364D19) corresponding to a region on chromosome 15 (32,291,106–32,463,964 relative to the hg19 human reference sequence).”