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.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Giordano F,Aigrain L,Quail MA,Coupland P,Bonfield JK,Davies RM,Tischler G,Jackson DK,Keane TM,Li J,Yue JX,Liti G,Durbin R,Ning Zdoi
10.1038/s41598-017-03996-zsubject
Has Abstractpub_date
2017-06-21 00:00:00pages
3935issue
1issn
2045-2322pii
10.1038/s41598-017-03996-zjournal_volume
7pub_type
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