Open Access Highly Accessed Research article

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

Marco Ferrarini1, Marco Moretto1, Judson A Ward2, Nada Šurbanovski1, Vladimir Stevanović3, Lara Giongo1, Roberto Viola1, Duccio Cavalieri1, Riccardo Velasco1, Alessandro Cestaro1 and Daniel J Sargent1*

Author Affiliations

1 Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy

2 Driscoll’s, 151 Silliman Road, Watsonville, CA 95077-5045 USA

3 Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Takovska 43, 11000 Belgrade, Serbia

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BMC Genomics 2013, 14:670  doi:10.1186/1471-2164-14-670

Published: 1 October 2013

Additional files

Additional file 1:

R scripts used to plot windows-based mean coverage against GC content in the PacBio and Illumiona datasets.

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Open Data

Additional file 2:

Python script used to calculate the mean error rate in the error-corrected PacBio reads from the BLAT alignment of the data against the chloroplast consensus sequence.

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Additional file 3:

Python script used to calculate the mean error rate in the Illumina raw reads from the SMALT alignment of the data against the chloroplast consensus sequence.

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Additional file 4:

Command line references for data processing and assembly performed in this study.

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Open Data