Authors
Inanc Birol, Anthony Raymond, Shaun D Jackman, Stephen Pleasance, Robin Coope, Greg A Taylor, Macaire Man Saint Yuen, Christopher I Keeling, Dana Brand, Benjamin P Vandervalk, Heather Kirk, Pawan Pandoh, Richard A Moore, Yongjun Zhao, Andrew J Mungall, Barry Jaquish, Alvin Yanchuk, Carol Ritland, Brian Boyle, Jean Bousquet, Kermit Ritland, John MacKay, Jörg Bohlmann, Steven JM Jones
Publication date
2013/6/15
Journal
Bioinformatics
Volume
29
Issue
12
Pages
1492-1497
Publisher
Oxford University Press
Description
White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft …
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