Genome Project Standards in a New Era of Sequencing

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For over a decade, genome 43 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 a careful 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 ... continued below

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Consortia, GSC; Consortia, HMP Jumpstart; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G. et al. June 1, 2009.

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For over a decade, genome 43 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 a careful 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 contributed to many wasted hours of (mis)interpretation. These same novel sequencing technologies have also brought an exponential leap in raw sequencing capability, and at greatly reduced prices that have further skewed the time- and cost-ratios of draft data generation versus the painstaking process of improving and finishing a genome. The resulting effect is an ever-widening gap between drafted and finished genomes that only promises to continue (Figure 1), hence there is an urgent need to distinguish good and poor datasets. The sequencing institutes in the authorship, along with the NIH's Human Microbiome Project Jumpstart Consortium (3), strongly believe that a new set of standards is required for genome sequences. The following represents a set of six community-defined categories of genome sequence standards that better reflect the quality of the genome sequence, based on our collective understanding of the different technologies, available assemblers, and the varied efforts to improve upon drafted genomes. Due to the increasingly rapid pace of genomics we avoided the use of rigid numerical thresholds in our definitions to take into account the types of products achieved by any combination of technology, chemistry, assembler, or improvement/finishing process.

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  • Journal Name: Science

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  • Report No.: LBNL-2718E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 974269
  • Archival Resource Key: ark:/67531/metadc929887

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  • June 1, 2009

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  • Nov. 13, 2016, 7:26 p.m.

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  • Nov. 18, 2016, 2:45 p.m.

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Consortia, GSC; Consortia, HMP Jumpstart; Chain, P. S. G.; Grafham, D. V.; Fulton, R. S.; FitzGerald, M. G. et al. Genome Project Standards in a New Era of Sequencing, article, June 1, 2009; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc929887/: accessed September 19, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.