2013
DOI: 10.1186/2047-217x-2-10
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Abstract: BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best as… Show more

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Cited by 605 publications
(549 citation statements)
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References 61 publications
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“…Second, further improvements of the assembly attributes were obtained by merging the single-platform assemblies. Previously, assembly merging with Metassembler was found to modestly improve the starting assemblies [Bradnam et al, 2013]. Here, we obtained large gains in the N50, with the PICR metassembly being ~4x more contiguous than the starting assemblies.…”
Section: Discussionmentioning
confidence: 52%
“…Second, further improvements of the assembly attributes were obtained by merging the single-platform assemblies. Previously, assembly merging with Metassembler was found to modestly improve the starting assemblies [Bradnam et al, 2013]. Here, we obtained large gains in the N50, with the PICR metassembly being ~4x more contiguous than the starting assemblies.…”
Section: Discussionmentioning
confidence: 52%
“…In total, 237 of 248 CEGs were completely present, and 7 CEGs were partially present, indicating that fewer than 2% of the CEGs could not be detected, which compared very favorably with other assemblies 31 .…”
Section: Assessment Of Genome Qualitymentioning
confidence: 83%
“…New reference-quality sequence sources are needed, because generation of finished sequence from clone libraries is in significant decline due to cost and some remaining assembly gaps occur in regions recalcitrant to cloning. A growing collection of human genomes in INSDC databases, a prerequisite for any sequence that will contribute to the reference assembly, that were sequenced and assembled with new technologies are candidates for use in assembly improvement (Earl et al 2011;Vezzi et al 2012;Bradnam et al 2013;English et al 2015;Pendleton et al 2015;Seo et al 2016;Shi et al 2016;Zook et al 2016). However, WGS assembly sequences have historically not been considered reference quality, raising concerns about their use in reference genome assembly curation.…”
Section: De Novo Assembly Evaluationsmentioning
confidence: 99%