Open Access Highly Accessed Research article

Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing

Sebastiaan van Heesch1, Wigard P Kloosterman2, Nico Lansu1, Frans-Paul Ruzius1, Elizabeth Levandowsky3, Clarence C Lee3, Shiguo Zhou4, Steve Goldstein4, David C Schwartz4, Timothy T Harkins3, Victor Guryev15* and Edwin Cuppen12*

Author Affiliations

1 Hubrecht Institute/KNAW and University Medical Center Utrecht, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands

2 Department of Medical Genetics, UMC Utrecht, Universiteitsweg 100, Utrecht, 3584 GG, The Netherlands

3 Life Technologies Inc., Advanced Applications Group, 500 Cummings Center, Beverly, MA, 01915, USA

4 Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA

5 Present address: Laboratory of Genome Structure and Ageing, European Research Institute for the Biology of Ageing; RuG and UMC Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands

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BMC Genomics 2013, 14:257  doi:10.1186/1471-2164-14-257

Published: 16 April 2013

Additional files

Additional file 1:

Size distribution of different types of LINE (L1) elements throughout the rat genome.

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Additional file 2:

Schematic outline of the generation of large insert mate-paired libraries.

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Additional file 3:

Table displaying the circularization efficiency of each individual library.

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Additional file 4:

Scaffolding results of contigs from the current rat reference genome assembly using all possible combinations of paired-read libraries.

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Additional file 5:

Combining insert sizes results in a more dramatic increase in N50 values than increasing only the physical coverage of one insert.

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Additional file 6:

Combinations of insert sizes improve scaffolding N50 values more than increasing the coverage of a single insert library.

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Additional file 7:

MP based scaffolding reveals inconsistencies with the current rat reference genome assembly.

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Additional file 8:

Inconsistent links on rat chromosome 18 (RNO18) both within scaffolds and between scaffolds, based on a comparison between MP-based scaffolding and the current reference genome.

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Additional file 9:

Comparison between the MP workflow of SOLiD 5500 and SOLiD V4.

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Additional file 10:

Adapting the large insert MP protocol for Illumina sequencing.

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