An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

BMC Genomics
Marco FerrariniDaniel J Sargent


Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased genome coverage leading to fragmented genome assemblies. The PacBio RS long-read sequencing platform offers the promise of increased read length and unbiased genome coverage and thus the potential to produce genome sequence data of a finished quality containing fewer gaps and longer contigs. However, these advantages come at a much greater cost per nucleotide and with a perceived increase in error-rate. In this investigation, we evaluated the performance of the PacBio RS sequencing platform through the sequencing and de novo assembly of the Potentilla micrantha chloroplast genome. Following error-correction, a total of 28,638 PacBio RS reads were recovered with a mean read length of 1,902 bp totalling 54,492,250 nucleotides and representing an average depth of coverage of 320× the chloroplast genome. The dataset covered the entire 154,959 bp of the chloroplast genome in a single contig (100% coverage) compared to seven contigs (90.59% coverage) recovered from an Illumina data, and revealed no bias in coverage of GC rich region...Continue Reading


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Feb 28, 2007·BMC Bioinformatics·Daniel D SommerMihai Pop
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Oct 28, 2008·Bioinformatics·Jason R MillerGranger Sutton
Nov 22, 2008·Science·John EidStephen Turner
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Nov 10, 2009·Nature Biotechnology·Carl W FullerDmitri V Vezenov
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Jul 29, 2011·The New England Journal of Medicine·David A RaskoMatthew K Waldor
Dec 20, 2011·Nature Biotechnology·Hugo Y K LamMichael Snyder
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