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. 2014 Jun 20;15:211. doi: 10.1186/1471-2105-15-211

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Copyright © 2014 Boetzer and Pirovano; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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The effect of PacBio RS long read coverage on genome closure. Results are displayed for SSPACE-LongRead based on the CLCbio draft assembly for 5 organisms. For all samples the addition of PacBio reads has a positive effect and leads to a significant contig reduction. In general a 50× coverage is sufficient to scaffold over most gaps, though ideally a 110-160× coverage is required to guarantee an optimal performance of our software. Arguably a higher coverage (>160×) leads to more fragmented genomes, which is likely due to the increased complexity of the assembly graph.