De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-12

AUTHORS

Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning

ABSTRACT

Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes. Recently, genome assemblies using Oxford Nanopore MinION data have attracted much attention due to the portability and low cost of this novel sequencing instrument. In this paper, we re-sequenced a well characterized genome, the Saccharomyces cerevisiae S288C strain using three different platforms: MinION, PacBio and MiSeq. We present a comprehensive metric comparison of assemblies generated by various pipelines and discuss how the platform associated data characteristics affect the assembly quality. With a given read depth of 31X, the assemblies from both Pacific Biosciences and Oxford Nanopore MinION show excellent continuity and completeness for the 16 nuclear chromosomes, but not for the mitochondrial genome, whose reconstruction still represents a significant challenge. More... »

PAGES

3935

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-017-03996-z

DOI

http://dx.doi.org/10.1038/s41598-017-03996-z

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1086055771

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28638050


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